New method for predicting estrogen receptor status utilizing breast MRI texture kinetic analysis

NASA Astrophysics Data System (ADS)

Chaudhury, Baishali; Hall, Lawrence O.; Goldgof, Dmitry B.; Gatenby, Robert A.; Gillies, Robert; Drukteinis, Jennifer S.

2014-03-01

Magnetic Resonance Imaging (MRI) of breast cancer typically shows that tumors are heterogeneous with spatial variations in blood flow and cell density. Here, we examine the potential link between clinical tumor imaging and the underlying evolutionary dynamics behind heterogeneity in the cellular expression of estrogen receptors (ER) in breast cancer. We assume, in an evolutionary environment, that ER expression will only occur in the presence of significant concentrations of estrogen, which is delivered via the blood stream. Thus, we hypothesize, the expression of ER in breast cancer cells will correlate with blood flow on gadolinium enhanced breast MRI. To test this hypothesis, we performed quantitative analysis of blood flow on dynamic contrast enhanced MRI (DCE-MRI) and correlated it with the ER status of the tumor. Here we present our analytic methods, which utilize a novel algorithm to analyze 20 volumetric DCE-MRI breast cancer tumors. The algorithm generates post initial enhancement (PIE) maps from DCE-MRI and then performs texture features extraction from the PIE map, feature selection, and finally classification of tumors into ER positive and ER negative status. The combined gray level co-occurrence matrices, gray level run length matrices and local binary pattern histogram features allow quantification of breast tumor heterogeneity. The algorithm predicted ER expression with an accuracy of 85% using a Naive Bayes classifier in leave-one-out cross-validation. Hence, we conclude that our data supports the hypothesis that imaging characteristics can, through application of evolutionary principles, provide insights into the cellular and molecular properties of cancer cells.

An evolutionary link between capsular biogenesis and surface motility in bacteria.

PubMed

Agrebi, Rym; Wartel, Morgane; Brochier-Armanet, Céline; Mignot, Tâm

2015-05-01

Studying the evolution of macromolecular assemblies is important to improve our understanding of how complex cellular structures evolved, and to identify the functional building blocks that are involved. Recent studies suggest that the macromolecular complexes that are involved in two distinct processes in Myxococcus xanthus - surface motility and sporulation - are derived from an ancestral polysaccharide capsule assembly system. In this Opinion article, we argue that the available data suggest that the motility machinery evolved from this capsule assembly system following a gene duplication event, a change in carbohydrate polymer specificity and the acquisition of additional proteins by the motility complex, all of which are key features that distinguish the motility and sporulation systems. Furthermore, the presence of intermediates of these systems in bacterial genomes suggests a testable evolutionary model for their emergence and spread.

The drug target genes show higher evolutionary conservation than non-target genes.

PubMed

Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Model of community emergence in weighted social networks

NASA Astrophysics Data System (ADS)

Kumpula, J. M.; Onnela, J.-P.; Saramäki, J.; Kertész, J.; Kaski, K.

2009-04-01

Over the years network theory has proven to be rapidly expanding methodology to investigate various complex systems and it has turned out to give quite unparalleled insight to their structure, function, and response through data analysis, modeling, and simulation. For social systems in particular the network approach has empirically revealed a modular structure due to interplay between the network topology and link weights between network nodes or individuals. This inspired us to develop a simple network model that could catch some salient features of mesoscopic community and macroscopic topology formation during network evolution. Our model is based on two fundamental mechanisms of network sociology for individuals to find new friends, namely cyclic closure and focal closure, which are mimicked by local search-link-reinforcement and random global attachment mechanisms, respectively. In addition we included to the model a node deletion mechanism by removing all its links simultaneously, which corresponds for an individual to depart from the network. Here we describe in detail the implementation of our model algorithm, which was found to be computationally efficient and produce many empirically observed features of large-scale social networks. Thus this model opens a new perspective for studying such collective social phenomena as spreading, structure formation, and evolutionary processes.

Evolution and development of brain networks: from Caenorhabditis elegans to Homo sapiens.

PubMed

Kaiser, Marcus; Varier, Sreedevi

2011-01-01

Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes involving a limited amount of tasks and modalities to complex functional and behavioral processing integrating different kinds of information from highly specialized tissue. However, studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. 'Small-world' topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms. In conclusion, evolutionary divergence leads to greater complexity while following essential developmental constraints.

Investigating evolutionary constraints on the detection of threatening stimuli in preschool children.

PubMed

Zsido, Andras N; Deak, Anita; Losonci, Adrienn; Stecina, Diana; Arato, Akos; Bernath, Laszlo

2018-04-01

Numerous objects and animals could be threatening, and thus, children learn to avoid them early. Spiders and syringes are among the most common targets of fears and phobias of the modern word. However, they are of different origins: while the former is evolutionary relevant, the latter is not. We sought to investigate the underlying mechanisms that make the quick detection of such stimuli possible and enable the impulse to avoid them in the future. The respective categories of threatening and non-threatening targets were similar in shape, while low-level visual features were controlled. Our results showed that children found threatening cues faster, irrespective of the evolutionary age of the cues. However, they detected non-threatening evolutionary targets faster than non-evolutionary ones. We suggest that the underlying mechanism may be different: general feature detection can account for finding evolutionary threatening cues quickly, while specific features detection is more appropriate for modern threatening stimuli. Copyright © 2018 Elsevier B.V. All rights reserved.

True-Triaxial Experimental Study of the Evolutionary Features of the Acoustic Emissions and Sounds of Rockburst Processes

NASA Astrophysics Data System (ADS)

Su, Guoshao; Shi, Yanjiong; Feng, Xiating; Jiang, Jianqing; Zhang, Jie; Jiang, Quan

2018-02-01

Rockbursts are markedly characterized by the ejection of rock fragments from host rocks at certain speeds. The rockburst process is always accompanied by acoustic signals that include acoustic emissions (AE) and sounds. A deep insight into the evolutionary features of AE and sound signals is important to improve the accuracy of rockburst prediction. To investigate the evolutionary features of AE and sound signals, rockburst tests on granite rock specimens under true-triaxial loading conditions were performed using an improved rockburst testing system, and the AE and sounds during rockburst development were recorded and analyzed. The results show that the evolutionary features of the AE and sound signals were obvious and similar. On the eve of a rockburst, a `quiescent period' could be observed in both the evolutionary process of the AE hits and the sound waveform. Furthermore, the time-dependent fractal dimensions of the AE hits and sound amplitude both showed a tendency to continuously decrease on the eve of the rockbursts. In addition, on the eve of the rockbursts, the main frequency of the AE and sound signals both showed decreasing trends, and the frequency spectrum distributions were both characterized by low amplitudes, wide frequency bands and multiple peak shapes. Thus, the evolutionary features of sound signals on the eve of rockbursts, as well as that of AE signals, can be used as beneficial information for rockburst prediction.

Classification of Medical Datasets Using SVMs with Hybrid Evolutionary Algorithms Based on Endocrine-Based Particle Swarm Optimization and Artificial Bee Colony Algorithms.

PubMed

Lin, Kuan-Cheng; Hsieh, Yi-Hsiu

2015-10-01

The classification and analysis of data is an important issue in today's research. Selecting a suitable set of features makes it possible to classify an enormous quantity of data quickly and efficiently. Feature selection is generally viewed as a problem of feature subset selection, such as combination optimization problems. Evolutionary algorithms using random search methods have proven highly effective in obtaining solutions to problems of optimization in a diversity of applications. In this study, we developed a hybrid evolutionary algorithm based on endocrine-based particle swarm optimization (EPSO) and artificial bee colony (ABC) algorithms in conjunction with a support vector machine (SVM) for the selection of optimal feature subsets for the classification of datasets. The results of experiments using specific UCI medical datasets demonstrate that the accuracy of the proposed hybrid evolutionary algorithm is superior to that of basic PSO, EPSO and ABC algorithms, with regard to classification accuracy using subsets with a reduced number of features.

How Can Evolution Learn?

PubMed

Watson, Richard A; Szathmáry, Eörs

2016-02-01

The theory of evolution links random variation and selection to incremental adaptation. In a different intellectual domain, learning theory links incremental adaptation (e.g., from positive and/or negative reinforcement) to intelligent behaviour. Specifically, learning theory explains how incremental adaptation can acquire knowledge from past experience and use it to direct future behaviours toward favourable outcomes. Until recently such cognitive learning seemed irrelevant to the 'uninformed' process of evolution. In our opinion, however, new results formally linking evolutionary processes to the principles of learning might provide solutions to several evolutionary puzzles - the evolution of evolvability, the evolution of ecological organisation, and evolutionary transitions in individuality. If so, the ability for evolution to learn might explain how it produces such apparently intelligent designs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Punctuated equilibrium as an emergent process and its modified thermodynamic characterization.

PubMed

Wosniack, M E; da Luz, M G E; Schulman, L S

2017-01-07

We address evolutionary dynamics and consider under which conditions the ecosystem interaction network allows punctuated equilibrium (i.e., alternation between hectic and quasi-stable phases). We focus on the links connecting various species and on the strength and sign of those links. For this study we consider the Tangled Nature model, which allows considerable flexibility and plasticity in the analysis of interspecies interactions. We find that it is necessary to have a proper balance of connectivity and interaction intensities so as to establish the kind of mutual cooperation and competition found in nature. It suggests evolutionary punctuated equilibrium as an emergent process, thus displaying features of complex systems. To explicitly demonstrate this fact we consider an extended form of thermodynamics, defining (for the present context) relevant out-of-equilibrium "collective" functions. We then show how to characterize the punctuated equilibrium through entropy-like and free energy-like quantities. Finally, from a close analogy to thermodynamic systems, we propose a protocol similar to simulated annealing. It is based on controlling the species' rate of mutation during the hectic periods, in this way enhancing the exploration of the genome space (similar to the known behavior of bacteria in stressful environments). This allows the system to more rapidly converge to long-duration quasi-stable phases. Copyright © 2016 Elsevier Ltd. All rights reserved.

Simulating natural selection in landscape genetics

Treesearch

E. L. Landguth; S. A. Cushman; N. Johnson

2012-01-01

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

Heterogeneity of link weight and the evolution of cooperation

NASA Astrophysics Data System (ADS)

Iwata, Manabu; Akiyama, Eizo

2016-04-01

In this paper, we investigate the effect of heterogeneity of link weight, heterogeneity of the frequency or amount of interactions among individuals, on the evolution of cooperation. Based on an analysis of the evolutionary prisoner's dilemma game on a weighted one-dimensional lattice network with intra-individual heterogeneity, we confirm that moderate level of link-weight heterogeneity can facilitate cooperation. Furthermore, we identify two key mechanisms by which link-weight heterogeneity promotes the evolution of cooperation: mechanisms for spread and maintenance of cooperation. We also derive the corresponding conditions under which the mechanisms can work through evolutionary dynamics.

Genetic architecture and balancing selection: the life and death of differentiated variants.

PubMed

Llaurens, Violaine; Whibley, Annabel; Joron, Mathieu

2017-05-01

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems. © 2017 John Wiley & Sons Ltd.

The Evolutionary Tempo of Sex Chromosome Degradation in Carica papaya.

PubMed

Wu, Meng; Moore, Richard C

2015-06-01

Genes on non-recombining heterogametic sex chromosomes may degrade over time through the irreversible accumulation of deleterious mutations. In papaya, the non-recombining male-specific region of the Y (MSY) consists of two evolutionary strata corresponding to chromosomal inversions occurring approximately 7.0 and 1.9 MYA. The step-wise recombination suppression between the papaya X and Y allows for a temporal examination of the degeneration progress of the young Y chromosome. Comparative evolutionary analyses of 55 X/Y gene pairs showed that Y-linked genes have more unfavorable substitutions than X-linked genes. However, this asymmetric evolutionary pattern is confined to the oldest stratum, and is only observed when recently evolved pseudogenes are included in the analysis, indicating a slow degeneration tempo of the papaya Y chromosome. Population genetic analyses of coding sequence variation of six Y-linked focal loci in the oldest evolutionary stratum detected an excess of nonsynonymous polymorphism and reduced codon bias relative to autosomal loci. However, this pattern was also observed for corresponding X-linked loci. Both the MSY and its corresponding X-specific region are pericentromeric where recombination has been shown to be greatly reduced. Like the MSY region, overall selective efficacy on the X-specific region may be reduced due to the interference of selective forces between highly linked loci, or the Hill-Robertson effect, that is accentuated in regions of low or suppressed recombination. Thus, a pattern of gene decay on the X-specific region may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants1[W][OA

PubMed Central

Jiang, Wen-kai; Liu, Yun-long; Xia, En-hua; Gao, Li-zhi

2013-01-01

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs. PMID:23396833

Comparison of geographic distributions of Irritable Bowel Syndrome with Inflammatory Bowel Disease fail to support common evolutionary roots: Irritable Bowel Syndrome and Inflammatory Bowel Diseases are not related by evolution.

PubMed

Szilagyi, Andrew; Xue, Xiaoqing

2018-01-01

Irritable Bowel Syndrome (IBS) shares overlapping symptoms and some features of pathogenesis with Inflammatory Bowel Diseases (IBD: Crohn's disease [CD], and Ulcerative Colitis [UC]). Geographic markers such as latitude/sunshine and more recently lactase population distributions are found to be correlated with IBD. As a result of clinical and pathogenic similarities between the 2 conditions, some authorities questioned whether a connection exists between them. We compare IBS directly with IBD, and indirectly with geographic markers associated with IBD, in order to evaluate possible evolutionary links between IBS and IBD. Similar correlations may link IBS as a precursor to IBD and possibly other conditions which are geographically connected with IBD. Data from four systematic reviews on IBD incidence and prevalence, IBS prevalence, and lactase distributions were included. Pearson's correlations were used for comparisons, with IBD values log-transformed because of skewed distribution. The articles provided 18-28 complete set of national data. Direct comparison between IBS and IBD showed no significant correlations (r = -0.14, r = -0.06 for CD and UC prevalence, r = -0.10 for CD incidence). Indirect comparisons also failed to show correlations of IBS with lactase distributions (r = -0.17), sunshine (r = -0.2) or latitude (r = 0.097); however, there was significant correlation between lactase distributions and CD incidence (r = -0.84), prevalence (r = -0.55) and UC prevalence (r = -0.59). Both sunshine (r= -0.53) and latitude (r = 0.58) are also significantly related to CD incidence. It is concluded that IBS and IBD do not follow similar global geographic patterns. This suggests a lack of an evolutionary genetic background coincident with emergence of lactase persistence. As well, vitamin D has no obvious impact on development of IBS. Similarities with IBD may result from sub groups (not yet identified) within the current Rome criteria of IBS. Alternatively limited intestinal gut-brain responses to host microbial interactions may result in similar overlap features in both. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary mysteries in meiosis.

PubMed

Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

2016-10-19

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

Evolutionary mysteries in meiosis

PubMed Central

2016-01-01

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often ‘weird’ features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes. This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’. PMID:27619705

A strategy with novel evolutionary features for the iterated prisoner's dilemma.

PubMed

Li, Jiawei; Kendall, Graham

2009-01-01

In recent iterated prisoner's dilemma tournaments, the most successful strategies were those that had identification mechanisms. By playing a predetermined sequence of moves and learning from their opponents' responses, these strategies managed to identify their opponents. We believe that these identification mechanisms may be very useful in evolutionary games. In this paper one such strategy, which we call collective strategy, is analyzed. Collective strategies apply a simple but efficient identification mechanism (that just distinguishes themselves from other strategies), and this mechanism allows them to only cooperate with their group members and defect against any others. In this way, collective strategies are able to maintain a stable population in evolutionary iterated prisoner's dilemma. By means of an invasion barrier, this strategy is compared with other strategies in evolutionary dynamics in order to demonstrate its evolutionary features. We also find that this collective behavior assists the evolution of cooperation in specific evolutionary environments.

Climate change and evolutionary adaptation.

PubMed

Hoffmann, Ary A; Sgrò, Carla M

2011-02-24

Evolutionary adaptation can be rapid and potentially help species counter stressful conditions or realize ecological opportunities arising from climate change. The challenges are to understand when evolution will occur and to identify potential evolutionary winners as well as losers, such as species lacking adaptive capacity living near physiological limits. Evolutionary processes also need to be incorporated into management programmes designed to minimize biodiversity loss under rapid climate change. These challenges can be met through realistic models of evolutionary change linked to experimental data across a range of taxa.

A paradigm for viewing biologic systems as scale-free networks based on energy efficiency: implications for present therapies and the future of evolution.

PubMed

Yun, Anthony J; Lee, Patrick Y; Doux, John D

2006-01-01

A network constitutes an abstract description of the relationships among entities, respectively termed links and nodes. If a power law describes the probability distribution of the number of links per node, the network is said to be scale-free. Scale-free networks feature link clustering around certain hubs based on preferential attachments that emerge due either to merit or legacy. Biologic systems ranging from sub-atomic to ecosystems represent scale-free networks in which energy efficiency forms the basis of preferential attachments. This paradigm engenders a novel scale-free network theory of evolution based on energy efficiency. As environmental flux induces fitness dislocations and compels a new meritocracy, new merit-based hubs emerge, previously merit-based hubs become legacy hubs, and network recalibration occurs to achieve system optimization. To date, Darwinian evolution, characterized by innovation sampling, variation, and selection through filtered termination, has enabled biologic progress through optimization of energy efficiency. However, as humans remodel their environment, increasing the level of unanticipated fitness dislocations and inducing evolutionary stress, the tendency of networks to exhibit inertia and retain legacy hubs engender maladaptations. Many modern diseases may fundamentally derive from these evolutionary displacements. Death itself may constitute a programmed adaptation, terminating individuals who represent legacy hubs and recalibrating the network. As memes replace genes as the basis of innovation, death itself has become a legacy hub. Post-Darwinian evolution may favor indefinite persistence to optimize energy efficiency. We describe strategies to reprogram or decommission legacy hubs that participate in human disease and death.

Physical characteristics and evolutionary trends of continental rifts

NASA Technical Reports Server (NTRS)

Ramberg, I. B.; Morgan, P.

1984-01-01

Rifts may be defined as zones beneath which the entire lithosphere has ruptured in extension. They are widespread and occur in a variety of tectonic settings, and range up to 2,600 m.y. in age. The object of this review is to highlight characteristic features of modern and ancient rifts, to emphasize differences and similarities in order to help characterize evolutionary trends, to identify physical conditions favorable for initiation as well as termination of rifting, and to provide constraints for future modeling studies of rifting. Rifts are characterized on the basis of their structural, geomorphic, magmatic and geophysical features and the diverse character of these features and their evolutionary trends through time are discussed. Mechanisms of rifting are critically examined in terms of the physical characteristics and evolutionary trends of rifts, and it is concluded that while simple models can give valuable insight into specific processes of rifting, individual rifts can rarely, if ever, be characterized by well defined trends predicted by these models. More data are required to clearly define evolutionary trends, and the models require development to incorporate the effects of lithospheric heterogeneities and complex geologic histories.

Evolution of disorder in Mediator complex and its functional relevance

PubMed Central

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K.

2016-01-01

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. PMID:26590257

Evolutionary origin of the turtle skull.

PubMed

Bever, G S; Lyson, Tyler R; Field, Daniel J; Bhullar, Bhart-Anjan S

2015-09-10

Transitional fossils informing the origin of turtles are among the most sought-after discoveries in palaeontology. Despite strong genomic evidence indicating that turtles evolved from within the diapsid radiation (which includes all other living reptiles), evidence of the inferred transformation between an ancestral turtle with an open, diapsid skull to the closed, anapsid condition of modern turtles remains elusive. Here we use high-resolution computed tomography and a novel character/taxon matrix to study the skull of Eunotosaurus africanus, a 260-million-year-old fossil reptile from the Karoo Basin of South Africa, whose distinctive postcranial skeleton shares many unique features with the shelled body plan of turtles. Scepticism regarding the status of Eunotosaurus as the earliest stem turtle arises from the possibility that these shell-related features are the products of evolutionary convergence. Our phylogenetic analyses indicate strong cranial support for Eunotosaurus as a critical transitional form in turtle evolution, thus fortifying a 40-million-year extension to the turtle stem and moving the ecological context of its origin back onto land. Furthermore, we find unexpected evidence that Eunotosaurus is a diapsid reptile in the process of becoming secondarily anapsid. This is important because categorizing the skull based on the number of openings in the complex of dermal bone covering the adductor chamber has long held sway in amniote systematics, and still represents a common organizational scheme for teaching the evolutionary history of the group. These discoveries allow us to articulate a detailed and testable hypothesis of fenestral closure along the turtle stem. Our results suggest that Eunotosaurus represents a crucially important link in a chain that will eventually lead to consilience in reptile systematics, paving the way for synthetic studies of amniote evolution and development.

Diverse circovirus-like genome architectures revealed by environmental metagenomics.

PubMed

Rosario, Karyna; Duffy, Siobain; Breitbart, Mya

2009-10-01

Single-stranded DNA (ssDNA) viruses with circular genomes are the smallest viruses known to infect eukaryotes. The present study identified 10 novel genomes similar to ssDNA circoviruses through data-mining of public viral metagenomes. The metagenomic libraries included samples from reclaimed water and three different marine environments (Chesapeake Bay, British Columbia coastal waters and Sargasso Sea). All the genomes have similarities to the replication (Rep) protein of circoviruses; however, only half have genomic features consistent with known circoviruses. Some of the genomes exhibit a mixture of genomic features associated with different families of ssDNA viruses (i.e. circoviruses, geminiviruses and parvoviruses). Unique genome architectures and phylogenetic analysis of the Rep protein suggest that these viruses belong to novel genera and/or families. Investigating the complex community of ssDNA viruses in the environment can lead to the discovery of divergent species and help elucidate evolutionary links between ssDNA viruses.

From computers to cultivation: reconceptualizing evolutionary psychology.

PubMed

Barrett, Louise; Pollet, Thomas V; Stulp, Gert

2014-01-01

Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on "cognitive integration" or the "extended mind hypothesis" in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human "mind-making" within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach.

Automatic feature design for optical character recognition using an evolutionary search procedure.

PubMed

Stentiford, F W

1985-03-01

An automatic evolutionary search is applied to the problem of feature extraction in an OCR application. A performance measure based on feature independence is used to generate features which do not appear to suffer from peaking effects [17]. Features are extracted from a training set of 30 600 machine printed 34 class alphanumeric characters derived from British mail. Classification results on the training set and a test set of 10 200 characters are reported for an increasing number of features. A 1.01 percent forced decision error rate is obtained on the test data using 316 features. The hardware implementation should be cheap and fast to operate. The performance compares favorably with current low cost OCR page readers.

A molecular signaling approach to linking intraspecific variation and macro-evolutionary patterns.

PubMed

Swanson, Eli M; Snell-Rood, Emilie C

2014-11-01

Macro-evolutionary comparisons are a valued tool in evolutionary biology. Nevertheless, our understanding of how systems involved in molecular signaling change in concert with phenotypic diversification has lagged. We argue that integrating our understanding of the evolution of molecular signaling systems with phylogenetic comparative methods is an important step toward understanding the processes linking variation among individuals with variation among species. Focusing mostly on the endocrine system, we discuss how the complexity and mechanistic nature of molecular signaling systems may influence the application and interpretation of macro-evolutionary comparisons. We also detail five hypotheses concerning the role that physiological mechanisms can play in shaping macro-evolutionary patterns, and discuss ways in which these hypotheses could influence phenotypic diversification. Finally, we review a series of tools able to analyze the complexity of physiological systems and the way they change in concert with the phenotypes for which they coordinate development. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Phylogenetic distribution and evolutionary dynamics of the sex determination genes doublesex and transformer in insects.

PubMed

Geuverink, E; Beukeboom, L W

2014-01-01

Sex determination in insects is characterized by a gene cascade that is conserved at the bottom but contains diverse primary signals at the top. The bottom master switch gene doublesex is found in all insects. Its upstream regulator transformer is present in the orders Hymenoptera, Coleoptera and Diptera, but has thus far not been found in Lepidoptera and in the basal lineages of Diptera. transformer is presumed to be ancestral to the holometabolous insects based on its shared domains and conserved features of autoregulation and sex-specific splicing. We interpret that its absence in basal lineages of Diptera and its order-specific conserved domains indicate multiple independent losses or recruitments into the sex determination cascade. Duplications of transformer are found in derived families within the Hymenoptera, characterized by their complementary sex determination mechanism. As duplications are not found in any other insect order, they appear linked to the haplodiploid reproduction of the Hymenoptera. Further phylogenetic analyses combined with functional studies are needed to understand the evolutionary history of the transformer gene among insects. © 2013 S. Karger AG, Basel.

Rape revisited: sexual violence against women in the former Yugoslavia.

PubMed

Valentich, M

1994-01-01

This article presents information on the rape of women in the former Yugoslavia, focusing more on Muslim women in Bosnia-Herzegovina, and examines the evolutionary, sociological, psychological, and feminist theories of this form of sexual violence. Using a case study approach, through documentation from newspapers and other media accounts, this paper investigated the sexual violence that featured strongly in the campaign of ethnic cleansing or genocide of Muslims in Bosnia-Herzegovina. It was noted that the variables of power, sex, and aggression in the context of war seem to be linked. This is particularly evident when authority legitimates sexual aggression. Without the backing of authority, some rape is expected, but not of such proportion or brutality. In terms of the theories, the evolutionary perspective appears to have limited applicability in explaining rape as an act of war. However, the feminist and macrosociological multivariate theories that focus on heterogeneity of the population, a cultural foundation of very traditional gender roles, and a historical tradition that legitimates sexual violence by armies in war-time, provide more persuasive insights.

The Influence of Life History and Sexual Dimorphism on Entheseal Changes in Modern Humans and African Great Apes

PubMed Central

Milella, Marco

2014-01-01

Entheseal changes have been widely studied with regard to their correlation to biomechanical stress and their usefulness for biocultural reconstructions. However, anthropological and medical studies have demonstrated the marked influence of both age and sex on the development of these features. Studies of entheseal changes are mostly aimed in testing functional hypotheses and are mostly focused on modern humans, with few data available for non-human primates. The lack of comparative studies on the effect of age and sex on entheseal changes represent a gap in our understanding of the evolutionary basis of both development and degeneration of the human musculoskeletal system. The aim of the present work is to compare age trajectories and patterns of sexual dimorphism in entheseal changes between modern humans and African great apes. To this end we analyzed 23 postcranial entheses in a human contemporary identified skeletal collection (N = 484) and compared the results with those obtained from the analysis of Pan (N = 50) and Gorilla (N = 47) skeletal specimens. Results highlight taxon-specific age trajectories possibly linked to differences in life history schedules and phyletic relationships. Robusticity trajectories separate Pan and modern humans from Gorilla, whereas enthesopathic patterns are unique in modern humans and possibly linked to their extended potential lifespan. Comparisons between sexes evidence a decreasing dimorphism in robusticity from Gorilla, to modern humans to Pan, which is likely linked to the role played by size, lifespan and physical activity on robusticity development. The present study confirms previous hypotheses on the possible relevance of EC in the study of life history, pointing moreover to their usefulness in evolutionary studies. PMID:25251439

Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates.

PubMed

Cañestro, Cristian; Albalat, Ricard; Irimia, Manuel; Garcia-Fernàndez, Jordi

2013-02-01

The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes duplicated in the vertebrate lineage have provided the grounds to support experimentally this link. This article reviews cases of gene duplications derived either from the 2R-WGD or from local gene duplication events in vertebrates, analyzing their impact on the evolution of developmental innovations. We analyze how gene regulatory networks can be rewired by the activity of transposable elements after genome duplications, discuss how different mechanisms of duplication might affect the fate of duplicated genes, and how the loss of gene duplicates might influence the fate of surviving paralogs. We also discuss the evolutionary relationships between gene duplication and alternative splicing, in particular in the vertebrate lineage. Finally, we discuss the role that the 2R-WGD might have played in the evolution of vertebrate developmental gene networks, paying special attention to those related to vertebrate key features such as neural crest cells, placodes, and the complex tripartite brain. In this context, we argue that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators. Copyright © 2013 Elsevier Ltd. All rights reserved.

The influence of life history and sexual dimorphism on entheseal changes in modern humans and African great apes.

PubMed

Milella, Marco

2014-01-01

Entheseal changes have been widely studied with regard to their correlation to biomechanical stress and their usefulness for biocultural reconstructions. However, anthropological and medical studies have demonstrated the marked influence of both age and sex on the development of these features. Studies of entheseal changes are mostly aimed in testing functional hypotheses and are mostly focused on modern humans, with few data available for non-human primates. The lack of comparative studies on the effect of age and sex on entheseal changes represent a gap in our understanding of the evolutionary basis of both development and degeneration of the human musculoskeletal system. The aim of the present work is to compare age trajectories and patterns of sexual dimorphism in entheseal changes between modern humans and African great apes. To this end we analyzed 23 postcranial entheses in a human contemporary identified skeletal collection (N = 484) and compared the results with those obtained from the analysis of Pan (N = 50) and Gorilla (N = 47) skeletal specimens. Results highlight taxon-specific age trajectories possibly linked to differences in life history schedules and phyletic relationships. Robusticity trajectories separate Pan and modern humans from Gorilla, whereas enthesopathic patterns are unique in modern humans and possibly linked to their extended potential lifespan. Comparisons between sexes evidence a decreasing dimorphism in robusticity from Gorilla, to modern humans to Pan, which is likely linked to the role played by size, lifespan and physical activity on robusticity development. The present study confirms previous hypotheses on the possible relevance of EC in the study of life history, pointing moreover to their usefulness in evolutionary studies.

Phylogenetic Analysis Supports the Aerobic-Capacity Model for the Evolution of Endothermy.

PubMed

Nespolo, Roberto F; Solano-Iguaran, Jaiber J; Bozinovic, Francisco

2017-01-01

The evolution of endothermy is a controversial topic in evolutionary biology, although several hypotheses have been proposed to explain it. To a great extent, the debate has centered on the aerobic-capacity model (AC model), an adaptive hypothesis involving maximum and resting rates of metabolism (MMR and RMR, respectively; hereafter "metabolic traits"). The AC model posits that MMR, a proxy of aerobic capacity and sustained activity, is the target of directional selection and that RMR is also influenced as a correlated response. Associated with this reasoning are the assumptions that (1) factorial aerobic scope (FAS; MMR/RMR) and net aerobic scope (NAS; MMR - RMR), two commonly used indexes of aerobic capacity, show different evolutionary optima and (2) the functional link between MMR and RMR is a basic design feature of vertebrates. To test these assumptions, we performed a comparative phylogenetic analysis in 176 vertebrate species, ranging from fish and amphibians to birds and mammals. Using disparity-through-time analysis, we also explored trait diversification and fitted different evolutionary models to study the evolution of metabolic traits. As predicted, we found (1) a positive phylogenetic correlation between RMR and MMR, (2) diversification of metabolic traits exceeding that of random-walk expectations, (3) that a model assuming selection fits the data better than alternative models, and (4) that a single evolutionary optimum best fits FAS data, whereas a model involving two optima (one for ectotherms and another for endotherms) is the best explanatory model for NAS. These results support the AC model and give novel information concerning the mode and tempo of physiological evolution of vertebrates.

Comparison of multiobjective evolutionary algorithms: empirical results.

PubMed

Zitzler, E; Deb, K; Thiele, L

2000-01-01

In this paper, we provide a systematic comparison of various evolutionary approaches to multiobjective optimization using six carefully chosen test functions. Each test function involves a particular feature that is known to cause difficulty in the evolutionary optimization process, mainly in converging to the Pareto-optimal front (e.g., multimodality and deception). By investigating these different problem features separately, it is possible to predict the kind of problems to which a certain technique is or is not well suited. However, in contrast to what was suspected beforehand, the experimental results indicate a hierarchy of the algorithms under consideration. Furthermore, the emerging effects are evidence that the suggested test functions provide sufficient complexity to compare multiobjective optimizers. Finally, elitism is shown to be an important factor for improving evolutionary multiobjective search.

Crossover between structured and well-mixed networks in an evolutionary prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Dai, Qionglin; Cheng, Hongyan; Li, Haihong; Li, Yuting; Zhang, Mei; Yang, Junzhong

2011-07-01

In a spatial evolutionary prisoner’s dilemma game (PDG), individuals interact with their neighbors and update their strategies according to some rules. As is well known, cooperators are destined to become extinct in a well-mixed population, whereas they could emerge and be sustained on a structured network. In this work, we introduce a simple model to investigate the crossover between a structured network and a well-mixed one in an evolutionary PDG. In the model, each link j is designated a rewiring parameter τj, which defines the time interval between two successive rewiring events for link j. By adjusting the rewiring parameter τ (the mean time interval for any link in the network), we could change a structured network into a well-mixed one. For the link rewiring events, three situations are considered: one synchronous situation and two asynchronous situations. Simulation results show that there are three regimes of τ: large τ where the density of cooperators ρc rises to ρc,∞ (the value of ρc for the case without link rewiring), small τ where the mean-field description for a well-mixed network is applicable, and moderate τ where the crossover between a structured network and a well-mixed one happens.

Group adaptation, formal darwinism and contextual analysis.

PubMed

Okasha, S; Paternotte, C

2012-06-01

We consider the question: under what circumstances can the concept of adaptation be applied to groups, rather than individuals? Gardner and Grafen (2009, J. Evol. Biol.22: 659-671) develop a novel approach to this question, building on Grafen's 'formal Darwinism' project, which defines adaptation in terms of links between evolutionary dynamics and optimization. They conclude that only clonal groups, and to a lesser extent groups in which reproductive competition is repressed, can be considered as adaptive units. We re-examine the conditions under which the selection-optimization links hold at the group level. We focus on an important distinction between two ways of understanding the links, which have different implications regarding group adaptationism. We show how the formal Darwinism approach can be reconciled with G.C. Williams' famous analysis of group adaptation, and we consider the relationships between group adaptation, the Price equation approach to multi-level selection, and the alternative approach based on contextual analysis. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Evolution of Bow-Tie Architectures in Biology

PubMed Central

Friedlander, Tamar; Mayo, Avraham E.; Tlusty, Tsvi; Alon, Uri

2015-01-01

Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. PMID:25798588

Evolution of disorder in Mediator complex and its functional relevance.

PubMed

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K

2016-02-29

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of 'junction-MoRF' has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein-protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

BrassiBase: introduction to a novel knowledge database on Brassicaceae evolution.

PubMed

Kiefer, Markus; Schmickl, Roswitha; German, Dmitry A; Mandáková, Terezie; Lysak, Martin A; Al-Shehbaz, Ihsan A; Franzke, Andreas; Mummenhoff, Klaus; Stamatakis, Alexandros; Koch, Marcus A

2014-01-01

The Brassicaceae family (mustards or crucifers) includes Arabidopsis thaliana as one of the most important model species in plant biology and a number of important crop plants such as the various Brassica species (e.g. cabbage, canola and mustard). Moreover, the family comprises an increasing number of species that serve as study systems in many fields of plant science and evolutionary research. However, the systematics and taxonomy of the family are very complex and access to scientifically valuable and reliable information linked to species and genus names and its interpretation are often difficult. BrassiBase is a continuously developing and growing knowledge database (http://brassibase.cos.uni-heidelberg.de) that aims at providing direct access to many different types of information ranging from taxonomy and systematics to phylo- and cytogenetics. Providing critically revised key information, the database intends to optimize comparative evolutionary research in this family and supports the introduction of the Brassicaceae as the model family for evolutionary biology and plant sciences. Some features that should help to accomplish these goals within a comprehensive taxonomic framework have now been implemented in the new version 1.1.9. A 'Phylogenetic Placement Tool' should help to identify critical accessions and germplasm and provide a first visualization of phylogenetic relationships. The 'Cytogenetics Tool' provides in-depth information on genome sizes, chromosome numbers and polyploidy, and sets this information into a Brassicaceae-wide context.

Evolutionary perspectives on the links between mitochondrial genotype and disease phenotype.

PubMed

Dowling, Damian K

2014-04-01

Disorders of the mitochondrial respiratory chain are heterogeneous in their symptoms and underlying genetics. Simple links between candidate mutations and expression of disease phenotype typically do not exist. It thus remains unclear how the genetic variation in the mitochondrial genome contributes to the phenotypic expression of complex traits and disease phenotypes. I summarize the basic genetic processes known to underpin mitochondrial disease. I highlight other plausible processes, drawn from the evolutionary biological literature, whose contribution to mitochondrial disease expression remains largely empirically unexplored. I highlight recent advances to the field, and discuss common-ground and -goals shared by researchers across medical and evolutionary domains. Mitochondrial genetic variance is linked to phenotypic variance across a variety of traits (e.g. reproductive function, life expectancy) fundamental to the upkeep of good health. Evolutionary theory predicts that mitochondrial genomes are destined to accumulate male-harming (but female-friendly) mutations, and this prediction has received proof-of-principle support. Furthermore, mitochondrial effects on the phenotype are typically manifested via interactions between mitochondrial and nuclear genes. Thus, whether a mitochondrial mutation is pathogenic in effect can depend on the nuclear genotype in which is it expressed. Many disease phenotypes associated with OXPHOS malfunction might be determined by the outcomes of mitochondrial-nuclear interactions, and by the evolutionary forces that historically shaped mitochondrial DNA (mtDNA) sequences. Concepts and results drawn from the evolutionary sciences can have broad, but currently under-utilized, applicability to the medical sciences and provide new insights into understanding the complex genetics of mitochondrial disease. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research. Copyright © 2013. Published by Elsevier B.V.

The ubiquilin gene family: evolutionary patterns and functional insights

PubMed Central

2014-01-01

Background Ubiquilins are proteins that function as ubiquitin receptors in eukaryotes. Mutations in two ubiquilin-encoding genes have been linked to the genesis of neurodegenerative diseases. However, ubiquilin functions are still poorly understood. Results In this study, evolutionary and functional data are combined to determine the origin and diversification of the ubiquilin gene family and to characterize novel potential roles of ubiquilins in mammalian species, including humans. The analysis of more than six hundred sequences allowed characterizing ubiquilin diversity in all the main eukaryotic groups. Many organisms (e. g. fungi, many animals) have single ubiquilin genes, but duplications in animal, plant, alveolate and excavate species are described. Seven different ubiquilins have been detected in vertebrates. Two of them, here called UBQLN5 and UBQLN6, had not been hitherto described. Significantly, marsupial and eutherian mammals have the most complex ubiquilin gene families, composed of up to 6 genes. This exceptional mammalian-specific expansion is the result of the recent emergence of four new genes, three of them (UBQLN3, UBQLN5 and UBQLNL) with precise testis-specific expression patterns that indicate roles in the postmeiotic stages of spermatogenesis. A gene with related features has independently arisen in species of the Drosophila genus. Positive selection acting on some mammalian ubiquilins has been detected. Conclusions The ubiquilin gene family is highly conserved in eukaryotes. The infrequent lineage-specific amplifications observed may be linked to the emergence of novel functions in particular tissues. PMID:24674348

Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures.

PubMed

Upadhyay, Mohita; Vivekanandan, Perumal

2015-01-01

Papillomaviruses and polyomaviruses are small ds-DNA viruses infecting a wide-range of vertebrate hosts. Evidence supporting co-evolution of the virus with the host does not fully explain the evolutionary path of papillomaviruses and polyomaviruses. Studies analyzing CpG dinucleotide frequencies in virus genomes have provided interesting insights on virus evolution. CpG dinucleotide depletion has not been extensively studied among papillomaviruses and polyomaviruses. We sought to analyze the relative abundance of dinucleotides and the relative roles of evolutionary pressures in papillomaviruses and polyomaviruses. We studied 127 full-length sequences from papillomaviruses and 56 full-length sequences from polyomaviruses. We analyzed the relative abundance of dinucleotides, effective codon number (ENC), differences in synonymous codon usage. We examined the association, if any, between the extent of CpG dinucleotide depletion and the evolutionary lineage of the infected host. We also investigated the contribution of mutational pressure and translational selection to the evolution of papillomaviruses and polyomaviruses. All papillomaviruses and polyomaviruses are CpG depleted. Interestingly, the evolutionary lineage of the infected host determines the extent of CpG depletion among papillomaviruses and polyomaviruses. CpG dinucleotide depletion was more pronounced among papillomaviruses and polyomaviruses infecting human and other mammals as compared to those infecting birds. Our findings demonstrate that CpG depletion among papillomaviruses is linked to mutational pressure; while CpG depletion among polyomaviruses is linked to translational selection. We also present evidence that suggests methylation of CpG dinucleotides may explain, at least in part, the depletion of CpG dinucleotides among papillomaviruses but not polyomaviruses. The extent of CpG depletion among papillomaviruses and polyomaviruses is linked to the evolutionary lineage of the infected host. Our results highlight the existence of divergent evolutionary pressures leading to CpG dinucleotide depletion among small ds-DNA viruses infecting vertebrate hosts.

From computers to cultivation: reconceptualizing evolutionary psychology

PubMed Central

Barrett, Louise; Pollet, Thomas V.; Stulp, Gert

2014-01-01

Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on “cognitive integration” or the “extended mind hypothesis” in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human “mind-making” within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach. PMID:25161633

Evolutionary biology: microsporidia sex--a missing link to fungi.

PubMed

Dyer, Paul S

2008-11-11

The evolutionary origins of the microsporidia, a group of intracellular eukaryotic pathogens, have been unclear. Genome analysis of a sex locus and other gene clusters has now revealed conserved synteny with zygomycete fungi, indicating that microsporidia are true fungi descended from a zygomycete ancestor.

Episodic processes, invasion and faunal mosaics in evolutionary and ecological time

USDA-ARS?s Scientific Manuscript database

Episodes of ecological perturbation and faunal turnover represent crises for global biodiversity and have occurred periodically across Earth history on a continuum linking deep evolutionary and shallow ecological time. Major extinction events and biodiversity crises across the 540 milion years of th...

Low X/Y divergence in four pairs of papaya sex-linked genes.

PubMed

Yu, Qingyi; Hou, Shaobin; Feltus, F Alex; Jones, Meghan R; Murray, Jan E; Veatch, Olivia; Lemke, Cornelia; Saw, Jimmy H; Moore, Richard C; Thimmapuram, Jyothi; Liu, Lei; Moore, Paul H; Alam, Maqsudul; Jiang, Jiming; Paterson, Andrew H; Ming, Ray

2008-01-01

Sex chromosomes in flowering plants, in contrast to those in animals, evolved relatively recently and only a few are heteromorphic. The homomorphic sex chromosomes of papaya show features of incipient sex chromosome evolution. We investigated the features of paired X- and Y-specific bacterial artificial chromosomes (BACs), and estimated the time of divergence in four pairs of sex-linked genes. We report the results of a comparative analysis of long contiguous genomic DNA sequences between the X and hermaphrodite Y (Y(h)) chromosomes. Numerous chromosomal rearrangements were detected in the male-specific region of the Y chromosome (MSY), including inversions, deletions, insertions, duplications and translocations, showing the dynamic evolutionary process on the MSY after recombination ceased. DNA sequence expansion was documented in the two regions of the MSY, demonstrating that the cytologically homomorphic sex chromosomes are heteromorphic at the molecular level. Analysis of sequence divergence between four X and Y(h) gene pairs resulted in a estimated age of divergence of between 0.5 and 2.2 million years, supporting a recent origin of the papaya sex chromosomes. Our findings indicate that sex chromosomes did not evolve at the family level in Caricaceae, and reinforce the theory that sex chromosomes evolve at the species level in some lineages.

Early Development and Orientation of the Acoustic Funnel Provides Insight into the Evolution of Sound Reception Pathways in Cetaceans

PubMed Central

Yamato, Maya; Pyenson, Nicholas D.

2015-01-01

Whales receive underwater sounds through a fundamentally different mechanism than their close terrestrial relatives. Instead of hearing through the ear canal, cetaceans hear through specialized fatty tissues leading to an evolutionarily novel feature: an acoustic funnel located anterior to the tympanic aperture. We traced the ontogenetic development of this feature in 56 fetal specimens from 10 different families of toothed (odontocete) and baleen (mysticete) whales, using X-ray computed tomography. We also charted ear ossification patterns through ontogeny to understand the impact of heterochronic developmental processes. We determined that the acoustic funnel arises from a prominent V-shaped structure established early in ontogeny, formed by the malleus and the goniale. In odontocetes, this V-formation develops into a cone-shaped funnel facing anteriorly, directly into intramandibular acoustic fats, which is likely functionally linked to the anterior orientation of sound reception in echolocation. In contrast, the acoustic funnel in balaenopterids rotates laterally, later in fetal development, consistent with a lateral sound reception pathway. Balaenids and several fossil mysticetes retain a somewhat anteriorly oriented acoustic funnel in the mature condition, indicating that a lateral sound reception pathway in balaenopterids may be a recent evolutionary innovation linked to specialized feeding modes, such as lunge-feeding. PMID:25760328

Somatic polyploidy is associated with the upregulation of c-MYC interacting genes and EMT-like signature

PubMed Central

Vazquez-Martin, Alejandro; Anatskaya, Olga V.; Giuliani, Alessandro; Erenpreisa, Jekaterina; Huang, Sui; Salmina, Kristine; Inashkina, Inna; Huna, Anda; Nikolsky, Nikolai N.; Vinogradov, Alexander E.

2016-01-01

The dependence of cancer on overexpressed c-MYC and its predisposition for polyploidy represents a double puzzle. We address this conundrum by cross-species transcription analysis of c-MYC interacting genes in polyploid vs. diploid tissues and cells, including human vs. mouse heart, mouse vs. human liver and purified 4n vs. 2n mouse decidua cells. Gene-by-gene transcriptome comparison and principal component analysis indicated that c-MYC interactants are significantly overrepresented among ploidy-associated genes. Protein interaction networks and gene module analysis revealed that the most upregulated genes relate to growth, stress response, proliferation, stemness and unicellularity, as well as to the pathways of cancer supported by MAPK and RAS coordinated pathways. A surprising feature was the up-regulation of epithelial-mesenchymal transition (EMT) modules embodied by the N-cadherin pathway and EMT regulators from SNAIL and TWIST families. Metabolic pathway analysis also revealed the EMT-linked features, such as global proteome remodeling, oxidative stress, DNA repair and Warburg-like energy metabolism. Genes associated with apoptosis, immunity, energy demand and tumour suppression were mostly down-regulated. Noteworthy, despite the association between polyploidy and ample features of cancer, polyploidy does not trigger it. Possibly it occurs because normal polyploidy does not go that far in embryonalisation and linked genome destabilisation. In general, the analysis of polyploid transcriptome explained the evolutionary relation of c-MYC and polyploidy to cancer. PMID:27655693

Systematic analysis and evolution of 5S ribosomal DNA in metazoans.

PubMed

Vierna, J; Wehner, S; Höner zu Siederdissen, C; Martínez-Lage, A; Marz, M

2013-11-01

Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12,766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

PubMed Central

Vierna, J; Wehner, S; Höner zu Siederdissen, C; Martínez-Lage, A; Marz, M

2013-01-01

Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12 766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades. PMID:23838690

Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

PubMed Central

Bryson, David M.; Ofria, Charles

2013-01-01

We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements in the majority of test environments, along with versions of each of the remaining architecture modifications that show significant improvements in multiple environments. However, some tested modifications were detrimental, though most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a broad range of challenges. PMID:24376669

Extraordinary Sequence Divergence at Tsga8, an X-linked Gene Involved in Mouse Spermiogenesis

PubMed Central

Good, Jeffrey M.; Vanderpool, Dan; Smith, Kimberly L.; Nachman, Michael W.

2011-01-01

The X chromosome plays an important role in both adaptive evolution and speciation. We used a molecular evolutionary screen of X-linked genes potentially involved in reproductive isolation in mice to identify putative targets of recurrent positive selection. We then sequenced five very rapidly evolving genes within and between several closely related species of mice in the genus Mus. All five genes were involved in male reproduction and four of the genes showed evidence of recurrent positive selection. The most remarkable evolutionary patterns were found at Testis-specific gene a8 (Tsga8), a spermatogenesis-specific gene expressed during postmeiotic chromatin condensation and nuclear transformation. Tsga8 was characterized by extremely high levels of insertion–deletion variation of an alanine-rich repetitive motif in natural populations of Mus domesticus and M. musculus, differing in length from the reference mouse genome by up to 89 amino acids (27% of the total protein length). This population-level variation was coupled with striking divergence in protein sequence and length between closely related mouse species. Although no clear orthologs had previously been described for Tsga8 in other mammalian species, we have identified a highly divergent hypothetical gene on the rat X chromosome that shares clear orthology with the 5′ and 3′ ends of Tsga8. Further inspection of this ortholog verified that it is expressed in rat testis and shares remarkable similarity with mouse Tsga8 across several general features of the protein sequence despite no conservation of nucleotide sequence across over 60% of the rat-coding domain. Overall, Tsga8 appears to be one of the most rapidly evolving genes to have been described in rodents. We discuss the potential evolutionary causes and functional implications of this extraordinary divergence and the possible contribution of Tsga8 and the other four genes we examined to reproductive isolation in mice. PMID:21186189

How Can We Study the Evolution of Animal Minds?

PubMed Central

Cauchoix, Maxime; Chaine, Alexis S.

2016-01-01

During the last 50 years, comparative cognition and neurosciences have improved our understanding of animal minds while evolutionary ecology has revealed how selection acts on traits through evolutionary time. We describe how cognition can be subject to natural selection like any other biological trait and how this evolutionary approach can be used to understand the evolution of animal cognition. We recount how comparative and fitness methods have been used to understand the evolution of cognition and outline how these approaches could extend our understanding of cognition. The fitness approach, in particular, offers unprecedented opportunities to study the evolutionary mechanisms responsible for variation in cognition within species and could allow us to investigate both proximate (i.e., neural and developmental) and ultimate (i.e., ecological and evolutionary) underpinnings of animal cognition together. We highlight recent studies that have successfully shown that cognitive traits can be under selection, in particular by linking individual variation in cognition to fitness. To bridge the gap between cognitive variation and fitness consequences and to better understand why and how selection can occur on cognition, we end this review by proposing a more integrative approach to study contemporary selection on cognitive traits combining socio-ecological data, minimally invasive neuroscience methods and measurement of ecologically relevant behaviors linked to fitness. Our overall goal in this review is to build a bridge between cognitive neuroscientists and evolutionary biologists, illustrate how their research could be complementary, and encourage evolutionary ecologists to include explicit attention to cognitive processes in their studies of behavior. PMID:27014163

An Evolutionary Framework for Understanding the Origin of Eukaryotes.

PubMed

Blackstone, Neil W

2016-04-27

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Evolutionary origins of leadership and followership.

PubMed

Van Vugt, Mark

2006-01-01

Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses.

Barnacle cement: a polymerization model based on evolutionary concepts

PubMed Central

Dickinson, Gary H.; Vega, Irving E.; Wahl, Kathryn J.; Orihuela, Beatriz; Beyley, Veronica; Rodriguez, Eva N.; Everett, Richard K.; Bonaventura, Joseph; Rittschof, Daniel

2009-01-01

Summary Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues. PMID:19837892

Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics.

PubMed

Bybee, Seth; Córdoba-Aguilar, Alex; Duryea, M Catherine; Futahashi, Ryo; Hansson, Bengt; Lorenzo-Carballa, M Olalla; Schilder, Ruud; Stoks, Robby; Suvorov, Anton; Svensson, Erik I; Swaegers, Janne; Takahashi, Yuma; Watts, Phillip C; Wellenreuther, Maren

2016-01-01

Odonata (dragonflies and damselflies) present an unparalleled insect model to integrate evolutionary genomics with ecology for the study of insect evolution. Key features of Odonata include their ancient phylogenetic position, extensive phenotypic and ecological diversity, several unique evolutionary innovations, ease of study in the wild and usefulness as bioindicators for freshwater ecosystems worldwide. In this review, we synthesize studies on the evolution, ecology and physiology of odonates, highlighting those areas where the integration of ecology with genomics would yield significant insights into the evolutionary processes that would not be gained easily by working on other animal groups. We argue that the unique features of this group combined with their complex life cycle, flight behaviour, diversity in ecological niches and their sensitivity to anthropogenic change make odonates a promising and fruitful taxon for genomics focused research. Future areas of research that deserve increased attention are also briefly outlined.

Neocortex expansion is linked to size variations in gene families with chemotaxis, cell-cell signalling and immune response functions in mammals.

PubMed

Castillo-Morales, Atahualpa; Monzón-Sandoval, Jimena; de Sousa, Alexandra A; Urrutia, Araxi O; Gutierrez, Humberto

2016-10-01

Increased brain size is thought to have played an important role in the evolution of mammals and is a highly variable trait across lineages. Variations in brain size are closely linked to corresponding variations in the size of the neocortex, a distinct mammalian evolutionary innovation. The genomic features that explain and/or accompany variations in the relative size of the neocortex remain unknown. By comparing the genomes of 28 mammalian species, we show that neocortical expansion relative to the rest of the brain is associated with variations in gene family size (GFS) of gene families that are significantly enriched in biological functions associated with chemotaxis, cell-cell signalling and immune response. Importantly, we find that previously reported GFS variations associated with increased brain size are largely accounted for by the stronger link between neocortex expansion and variations in the size of gene families. Moreover, genes within these families are more prominently expressed in the human neocortex during early compared with adult development. These results suggest that changes in GFS underlie morphological adaptations during brain evolution in mammalian lineages. © 2016 The Authors.

Neocortex expansion is linked to size variations in gene families with chemotaxis, cell–cell signalling and immune response functions in mammals

PubMed Central

Castillo-Morales, Atahualpa; Monzón-Sandoval, Jimena; de Sousa, Alexandra A.

2016-01-01

Increased brain size is thought to have played an important role in the evolution of mammals and is a highly variable trait across lineages. Variations in brain size are closely linked to corresponding variations in the size of the neocortex, a distinct mammalian evolutionary innovation. The genomic features that explain and/or accompany variations in the relative size of the neocortex remain unknown. By comparing the genomes of 28 mammalian species, we show that neocortical expansion relative to the rest of the brain is associated with variations in gene family size (GFS) of gene families that are significantly enriched in biological functions associated with chemotaxis, cell–cell signalling and immune response. Importantly, we find that previously reported GFS variations associated with increased brain size are largely accounted for by the stronger link between neocortex expansion and variations in the size of gene families. Moreover, genes within these families are more prominently expressed in the human neocortex during early compared with adult development. These results suggest that changes in GFS underlie morphological adaptations during brain evolution in mammalian lineages. PMID:27707894

Fossil traces of the bone-eating worm Osedax in early Oligocene whale bones

PubMed Central

Kiel, Steffen; Goedert, James L.; Kahl, Wolf-Achim; Rouse, Greg W.

2010-01-01

Osedax is a recently discovered group of siboglinid annelids that consume bones on the seafloor and whose evolutionary origins have been linked with Cretaceous marine reptiles or to the post-Cretaceous rise of whales. Here we present whale bones from early Oligocene bathyal sediments exposed in Washington State, which show traces similar to those made by Osedax today. The geologic age of these trace fossils (∼30 million years) coincides with the first major radiation of whales, consistent with the hypothesis of an evolutionary link between Osedax and its main food source, although older fossils should certainly be studied. Osedax has been destroying bones for most of the evolutionary history of whales and the possible significance of this “Osedax effect” in relation to the quality and quantity of their fossils is only now recognized. PMID:20424110

Preliminary Volcanic Feature Analysis of Olympus Mons and Ascraeus Mons, Mars

NASA Astrophysics Data System (ADS)

Mohr, K. J.; Williams, D. A.; Garry, W. B.; Bleacher, J. E.

2018-06-01

Geologic mapping has shown similar volcanic features observed on Olympus and Ascraeus Mons. These features are found on the same flanks, suggesting a similar evolutionary process for formation of the edifices.

A real negative selection algorithm with evolutionary preference for anomaly detection

NASA Astrophysics Data System (ADS)

Yang, Tao; Chen, Wen; Li, Tao

2017-04-01

Traditional real negative selection algorithms (RNSAs) adopt the estimated coverage (c0) as the algorithm termination threshold, and generate detectors randomly. With increasing dimensions, the data samples could reside in the low-dimensional subspace, so that the traditional detectors cannot effectively distinguish these samples. Furthermore, in high-dimensional feature space, c0 cannot exactly reflect the detectors set coverage rate for the nonself space, and it could lead the algorithm to be terminated unexpectedly when the number of detectors is insufficient. These shortcomings make the traditional RNSAs to perform poorly in high-dimensional feature space. Based upon "evolutionary preference" theory in immunology, this paper presents a real negative selection algorithm with evolutionary preference (RNSAP). RNSAP utilizes the "unknown nonself space", "low-dimensional target subspace" and "known nonself feature" as the evolutionary preference to guide the generation of detectors, thus ensuring the detectors can cover the nonself space more effectively. Besides, RNSAP uses redundancy to replace c0 as the termination threshold, in this way RNSAP can generate adequate detectors under a proper convergence rate. The theoretical analysis and experimental result demonstrate that, compared to the classical RNSA (V-detector), RNSAP can achieve a higher detection rate, but with less detectors and computing cost.

Evolution of complex life cycles in trophically transmitted helminths. I. Host incorporation and trophic ascent.

PubMed

Parker, G A; Ball, M A; Chubb, J C

2015-02-01

Links between parasites and food webs are evolutionarily ancient but dynamic: life history theory provides insights into helminth complex life cycle origins. Most adult helminths benefit by sexual reproduction in vertebrates, often high up food chains, but direct infection is commonly constrained by a trophic vacuum between free-living propagules and definitive hosts. Intermediate hosts fill this vacuum, facilitating transmission to definitive hosts. The central question concerns why sexual reproduction, and sometimes even larval growth, is suppressed in intermediate hosts, favouring growth arrest at larval maturity in intermediate hosts and reproductive suppression until transmission to definitive hosts? Increased longevity and higher growth in definitive hosts can generate selection for larger parasite body size and higher fecundity at sexual maturity. Life cycle length is increased by two evolutionary mechanisms, upward and downward incorporation, allowing simple (one-host) cycles to become complex (multihost). In downward incorporation, an intermediate host is added below the definitive host: models suggest that downward incorporation probably evolves only after ecological or evolutionary perturbations create a trophic vacuum. In upward incorporation, a new definitive host is added above the original definitive host, which subsequently becomes an intermediate host, again maintained by the trophic vacuum: theory suggests that this is plausible even under constant ecological/evolutionary conditions. The final cycle is similar irrespective of its origin (upward or downward). Insights about host incorporation are best gained by linking comparative phylogenetic analyses (describing evolutionary history) with evolutionary models (examining selective forces). Ascent of host trophic levels and evolution of optimal host taxa ranges are discussed. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Agency, Values, and Well-Being: A Human Development Model

ERIC Educational Resources Information Center

Welzel, Christian; Inglehart, Ronald

2010-01-01

This paper argues that feelings of agency are linked to human well-being through a sequence of adaptive mechanisms that promote human development, once existential conditions become permissive. In the first part, we elaborate on the evolutionary logic of this model and outline why an evolutionary perspective is helpful to understand changes in…

Metaphors--Messengers of Meaning: A Contribution to an Evolutionary Sociology of Science.

ERIC Educational Resources Information Center

Maasen, Sabine; Weingart, Peter

1995-01-01

Presents the idea that the central link between science and society is established by a diffusion of knowledge. Suggests knowledge transfers may be analyzed in a metaphorical context and that a metaphorical analysis should be combined with discourse analysis and central concepts of evolutionary theory. (50 references) (Author/AEF)

Resistance and relatedness on an evolutionary graph

PubMed Central

Maciejewski, Wes

2012-01-01

When investigating evolution in structured populations, it is often convenient to consider the population as an evolutionary graph—individuals as nodes, and whom they may act with as edges. There has, in recent years, been a surge of interest in evolutionary graphs, especially in the study of the evolution of social behaviours. An inclusive fitness framework is best suited for this type of study. A central requirement for an inclusive fitness analysis is an expression for the genetic similarity between individuals residing on the graph. This has been a major hindrance for work in this area as highly technical mathematics are often required. Here, I derive a result that links genetic relatedness between haploid individuals on an evolutionary graph to the resistance between vertices on a corresponding electrical network. An example that demonstrates the potential computational advantage of this result over contemporary approaches is provided. This result offers more, however, to the study of population genetics than strictly computationally efficient methods. By establishing a link between gene transfer and electric circuit theory, conceptualizations of the latter can enhance understanding of the former. PMID:21849384

Population genetics inside a cell: Mutations and mitochondrial genome maintenance

NASA Astrophysics Data System (ADS)

Goyal, Sidhartha; Shraiman, Boris; Gottschling, Dan

2012-02-01

In realistic ecological and evolutionary systems natural selection acts on multiple levels, i.e. it acts on individuals as well as on collection of individuals. An understanding of evolutionary dynamics of such systems is limited in large part due to the lack of experimental systems that can challenge theoretical models. Mitochondrial genomes (mtDNA) are subjected to selection acting on cellular as well as organelle levels. It is well accepted that mtDNA in yeast Saccharomyces cerevisiae is unstable and can degrade over time scales comparable to yeast cell division time. We utilize a recent technology designed in Gottschling lab to extract DNA from populations of aged yeast cells and deep sequencing to characterize mtDNA variation in a population of young and old cells. In tandem, we developed a stochastic model that includes the essential features of mitochondrial biology that provides a null model for expected mtDNA variation. Overall, we find approximately 2% of the polymorphic loci that show significant increase in frequency as cells age providing direct evidence for organelle level selection. Such quantitative study of mtDNA dynamics is absolutely essential to understand the propagation of mtDNA mutations linked to a spectrum of age-related diseases in humans.

HBC-Evo: predicting human breast cancer by exploiting amino acid sequence-based feature spaces and evolutionary ensemble system.

PubMed

Majid, Abdul; Ali, Safdar

2015-01-01

We developed genetic programming (GP)-based evolutionary ensemble system for the early diagnosis, prognosis and prediction of human breast cancer. This system has effectively exploited the diversity in feature and decision spaces. First, individual learners are trained in different feature spaces using physicochemical properties of protein amino acids. Their predictions are then stacked to develop the best solution during GP evolution process. Finally, results for HBC-Evo system are obtained with optimal threshold, which is computed using particle swarm optimization. Our novel approach has demonstrated promising results compared to state of the art approaches.

Nuclear hormone receptors in parasitic helminths

PubMed Central

Wu, Wenjie; LoVerde, Philip T

2010-01-01

Nuclear receptors (NRs) belong to a large protein superfamily that are important transcriptional modulators in metazoans. Parasitic helminths include parasitic worms from the Lophotrochozoa (Platyhelminths) and Ecdysozoa (Nematoda). NRs in parasitic helminths diverged into two different evolutionary lineages. NRs in parasitic Platyhelminths have orthologues in Deuterostomes, in arthropods or both with a feature of extensive gene loss and gene duplication within different gene groups. NRs in parasitic Nematoda follow the nematode evolutionary lineage with a feature of multiple duplication of SupNRs and gene loss. PMID:20600585

An Evolutionary Framework for Understanding the Origin of Eukaryotes

PubMed Central

Blackstone, Neil W.

2016-01-01

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

The Evolution of Ion Pumps.

ERIC Educational Resources Information Center

Maloney, Peter C.; Wilson, T. Hastings

1985-01-01

Constructs an evolutionary sequence to account for the diversity of ion pumps found today. Explanations include primary ion pumps in bacteria, features and distribution of ATP-driven pumps, preference for cation transport, and proton pump reversal. The integrated evolutionary hypothesis should encourage new experimental approaches. (DH)

Meiotic drive influences the outcome of sexually antagonistic selection at a linked locus.

PubMed

Patten, M M

2014-11-01

Most meiotic drivers, such as the t-haplotype in Mus and the segregation distorter (SD) in Drosophila, act in a sex-specific manner, gaining a transmission advantage through one sex although suffering only the fitness costs associated with the driver in the other. Their inheritance is thus more likely through one of the two sexes, a property they share with sexually antagonistic alleles. Previous theory has shown that pairs of linked loci segregating for sexually antagonistic alleles are more likely to remain polymorphic and that linkage disequilibrium accrues between them. I probe this similarity between drive and sexual antagonism and examine the evolution of chromosomes experiencing these selection pressures simultaneously. Reminiscent of previous theory, I find that: the opportunity for polymorphism increases for a sexually antagonistic locus that is physically linked to a driving locus; the opportunity for polymorphism at a driving locus also increases when linked to a sexually antagonistic locus; and stable linkage disequilibrium accompanies any polymorphic equilibrium. Additionally, I find that drive at a linked locus favours the fixation of sexually antagonistic alleles that benefit the sex in which drive occurs. Further, I show that under certain conditions reduced recombination between these two loci is selectively favoured. These theoretical results provide clear, testable predictions about the nature of sexually antagonistic variation on driving chromosomes and have implications for the evolution of genomic architecture. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Impressions of Danger Influence Impressions of People: An Evolutionary Perspective on Individual and Collective Cognition

PubMed Central

Schaller, Mark; Faulkner, Jason; Park, Justin H.; Neuberg, Steven L.; Kenrick, Douglas T.

2011-01-01

An evolutionary approach to social cognition yields novel hypotheses about the perception of people belonging to specific kinds of social categories. These implications are illustrated by empirical results linking the perceived threat of physical injury to stereotypical impressions of outgroups. We review a set of studies revealing several ways in which threat-connoting cues influence perceptions of ethnic outgroups and the individuals who belong to those outgroups. We also present new results that suggest additional implications of evolved danger-avoidance mechanisms on interpersonal communication and the persistence of cultural-level stereotypes about ethnic outgroups. The conceptual utility of an evolutionary approach is further illustrated by a parallel line of research linking the threat of disease to additional kinds of social perceptions and behaviors. Evolved danger-avoidance mechanisms appear to contribute in diverse ways to individual-level cognitive processes, as well as to culturally-shared collective beliefs. PMID:21874126

Regulatory divergence of X-linked genes and hybrid male sterility in mice.

PubMed

Oka, Ayako; Shiroishi, Toshihiko

2014-01-01

Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schürpf, Thomas; Chen, Qiang; Liu, Jin-huan

Developmental endothelial cell locus-1 (Del-1) glycoprotein is secreted by endothelial cells and a subset of macrophages. Del-1 plays a regulatory role in vascular remodeling and functions in innate immunity through interaction with integrin {alpha}{sub V}{beta}{sub 3}. Del-1 contains 3 epidermal growth factor (EGF)-like repeats and 2 discoidin-like domains. An Arg-Gly-Asp (RGD) motif in the second EGF domain (EGF2) mediates adhesion by endothelial cells and phagocytes. We report the crystal structure of its 3 EGF domains. The RGD motif of EGF2 forms a type II' {beta} turn at the tip of a long protruding loop, dubbed the RGD finger. Whereas EGF2more » and EGF3 constitute a rigid rod via an interdomain calcium ion binding site, the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1. Two unique O-linked glycans and 1 N-linked glycan locate to the opposite side of EGF2 from the RGD motif. These structural features favor integrin binding of the RGD finger. Mutagenesis data confirm the importance of having the RGD motif at the tip of the RGD finger. A database search for EGF domain sequences shows that this RGD finger is likely an evolutionary insertion and unique to the EGF domain of Del-1 and its homologue milk fat globule-EGF 8. The RGD finger of Del-1 is a unique structural feature critical for integrin binding.« less

Measuring the Acceptance of Evolutionary Theory in Texas 2-Year Colleges

ERIC Educational Resources Information Center

Brown, Jack; Scott, Joyce A.

2016-01-01

Evolutionary theory is the central unifying theory of the life sciences. However, acceptance and understanding of the theory have been found to be lacking in the general public, high school, and university populations. Prior research has linked low acceptance of the theory to a poor knowledge base in evolution, to the nature of science, and to…

Remembering the Forest While Viewing the Trees: Evolutionary Thinking in the Teaching of Molecular Biology

ERIC Educational Resources Information Center

Saraswati, Sitaraman; Sitaraman, Ramakrishnan

2014-01-01

Given the centrality of evolutionary theory to the study of biology, we present a strategy for reinforcing its importance by appropriately recontextualizing classic and well-known experiments that are not explicitly linked with evolution in conventional texts. This exercise gives students an appreciation of the applicability of the theory of…

Molecular evolution of the clustered MMIC-3 multigene family of Gossypium species

USDA-ARS?s Scientific Manuscript database

Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 supergene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate supergenes in allopolyploids. Here we report molecular evolutionary rates...

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

PubMed Central

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

2014-01-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

Why don’t you use Evolutionary Algorithms in Big Data?

NASA Astrophysics Data System (ADS)

Stanovov, Vladimir; Brester, Christina; Kolehmainen, Mikko; Semenkina, Olga

2017-02-01

In this paper we raise the question of using evolutionary algorithms in the area of Big Data processing. We show that evolutionary algorithms provide evident advantages due to their high scalability and flexibility, their ability to solve global optimization problems and optimize several criteria at the same time for feature selection, instance selection and other data reduction problems. In particular, we consider the usage of evolutionary algorithms with all kinds of machine learning tools, such as neural networks and fuzzy systems. All our examples prove that Evolutionary Machine Learning is becoming more and more important in data analysis and we expect to see the further development of this field especially in respect to Big Data.

Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing

PubMed Central

Sloan, Katherine E.; Mattijssen, Sandy; Lebaron, Simon; Tollervey, David; Pruijn, Ger J.M.

2013-01-01

Human ribosome production is up-regulated during tumorogenesis and is defective in many genetic diseases (ribosomopathies). We have undertaken a detailed analysis of human precursor ribosomal RNA (pre-rRNA) processing because surprisingly little is known about this important pathway. Processing in internal transcribed spacer 1 (ITS1) is a key step that separates the rRNA components of the large and small ribosomal subunits. We report that this was initiated by endonuclease cleavage, which required large subunit biogenesis factors. This was followed by 3′ to 5′ exonucleolytic processing by RRP6 and the exosome, an enzyme complex not previously linked to ITS1 removal. In contrast, RNA interference–mediated knockdown of the endoribonuclease MRP did not result in a clear defect in ITS1 processing. Despite the apparently high evolutionary conservation of the pre-rRNA processing pathway and ribosome synthesis factors, each of these features of human ITS1 processing is distinct from those in budding yeast. These results also provide significant insight into the links between ribosomopathies and ribosome production in human cells. PMID:23439679

A sex-ratio meiotic drive system in Drosophila simulans. II: an X-linked distorter.

PubMed

Tao, Yun; Araripe, Luciana; Kingan, Sarah B; Ke, Yeyan; Xiao, Hailian; Hartl, Daniel L

2007-11-06

The evolution of heteromorphic sex chromosomes creates a genetic condition favoring the invasion of sex-ratio meiotic drive elements, resulting in the biased transmission of one sex chromosome over the other, in violation of Mendel's first law. The molecular mechanisms of sex-ratio meiotic drive may therefore help us to understand the evolutionary forces shaping the meiotic behavior of the sex chromosomes. Here we characterize a sex-ratio distorter on the X chromosome (Dox) in Drosophila simulans by genetic and molecular means. Intriguingly, Dox has very limited coding capacity. It evolved from another X-linked gene, which also evolved de nova. Through retrotransposition, Dox also gave rise to an autosomal suppressor, not much yang (Nmy). An RNA interference mechanism seems to be involved in the suppression of the Dox distorter by the Nmy suppressor. Double mutant males of the genotype dox; nmy are normal for both sex-ratio and spermatogenesis. We postulate that recurrent bouts of sex-ratio meiotic drive and its subsequent suppression might underlie several common features observed in the heterogametic sex, including meiotic sex chromosome inactivation and achiasmy.

Common evolutionary trends underlie the four-bar linkage systems of sunfish and mantis shrimp.

PubMed

Hu, Yinan; Nelson-Maney, Nathan; Anderson, Philip S L

2017-05-01

Comparative biomechanics offers an opportunity to explore the evolution of disparate biological systems that share common underlying mechanics. Four-bar linkage modeling has been applied to various biological systems such as fish jaws and crustacean appendages to explore the relationship between biomechanics and evolutionary diversification. Mechanical sensitivity states that the functional output of a mechanical system will show differential sensitivity to changes in specific morphological components. We document similar patterns of mechanical sensitivity in two disparate four-bar systems from different phyla: the opercular four-bar system in centrarchid fishes and the raptorial appendage of stomatopods. We built dynamic linkage models of 19 centrarchid and 36 stomatopod species and used phylogenetic generalized least squares regression (PGLS) to compare evolutionary shifts in linkage morphology and mechanical outputs derived from the models. In both systems, the kinematics of the four-bar mechanism show significant evolutionary correlation with the output link, while travel distance of the output arm is correlated with the coupler link. This common evolutionary pattern seen in both fish and crustacean taxa is a potential consequence of the mechanical principles underlying four-bar systems. Our results illustrate the potential influence of physical principles on morphological evolution across biological systems with different structures, behaviors, and ecologies. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Development links psychological causes to evolutionary explanations.

PubMed

Fedyk, Mark; Kushnir, Tamar

2014-04-01

Our conscious abilities are learned in environments that have evolved to support them. This insight provides an alternative way of framing Huang & Bargh's (H&B's) provocative hypothesis. To understand the conflict between unconscious goals and consciousness, we can study the emergence of conscious thought and control in childhood. These developmental processes are also central to the best available current evolutionary theories.

Darwin's "Imaginary Illustrations": Creatively Teaching Evolutionary Concepts & the Nature of Science

ERIC Educational Resources Information Center

Love, Alan C.

2010-01-01

An overlooked feature of Darwin's work is his use of "imaginary illustrations" to show that natural selection is competent to produce adaptive, evolutionary change. When set in the context of Darwin's methodology, these thought experiments provide a novel way to teach natural selection and the nature of science.

A Coevolutionary Arms Race: Understanding Plant-Herbivore Interactions

ERIC Educational Resources Information Center

Becklin, Katie M.

2008-01-01

Plants and insects share a long evolutionary history characterized by relationships that affect individual, population, and community dynamics. Plant-herbivore interactions are a prominent feature of this evolutionary history; it is by plant-herbivore interactions that energy is transferred from primary producers to the rest of the food web. Not…

Molecular Evolution of Clustered MIC-3 (Meloidogyne Induced Cotton -3) Multigene Family of Gossypium Species

USDA-ARS?s Scientific Manuscript database

Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 multigene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate genes in allopolyploids. Here we report molecular evolutionary rates of t...

Decontaminate feature for tracking: adaptive tracking via evolutionary feature subset

NASA Astrophysics Data System (ADS)

Liu, Qiaoyuan; Wang, Yuru; Yin, Minghao; Ren, Jinchang; Li, Ruizhi

2017-11-01

Although various visual tracking algorithms have been proposed in the last 2-3 decades, it remains a challenging problem for effective tracking with fast motion, deformation, occlusion, etc. Under complex tracking conditions, most tracking models are not discriminative and adaptive enough. When the combined feature vectors are inputted to the visual models, this may lead to redundancy causing low efficiency and ambiguity causing poor performance. An effective tracking algorithm is proposed to decontaminate features for each video sequence adaptively, where the visual modeling is treated as an optimization problem from the perspective of evolution. Every feature vector is compared to a biological individual and then decontaminated via classical evolutionary algorithms. With the optimized subsets of features, the "curse of dimensionality" has been avoided while the accuracy of the visual model has been improved. The proposed algorithm has been tested on several publicly available datasets with various tracking challenges and benchmarked with a number of state-of-the-art approaches. The comprehensive experiments have demonstrated the efficacy of the proposed methodology.

[Creativity and psychiatric disorders: exploring a marginal area].

PubMed

Thys, E; Sabbe, B; De Hert, M

2012-01-01

Creativity is an important human quality on which many of man’s achievements are based. To give a historical and cultural context, to facilitate meaningful scientific research into the link between creativity and psychiatric disorders. Review of relevant literature. The possibility of a link between creativity and psychiatric vulnerability was first discussed in antiquity. Modern interest in the subject stems from the romantic era and acquired a scientific aura in the 19th century. In the 20th century creativity and psychopathology became still further entangled as a result of the influence that mentally disturbed artists exerted on art. The history of the Prinzhorn collection illustrates many aspects of this interaction. Psychometric, psychodiagnostic and genetic research supports a link between creativity and psychiatric illness within the bipolar-psychotic continuum, with schizotypy/thymotypy as prototypes of creativity-related disorders. Evolutionary hypotheses connect the schizophrenia paradox to a survival advantage obtained as a result of enhanced creative ability. Neuro-aesthetics explains the neurologic correlates of the aesthetic experience on the basis of the features of the visual system. A specific challenge for scientific research in this complex and heterogeneous area is appropriate operationalisation of creativity and psychiatric illness within an truly artistic context. There is a continuing need for meaningful definitions and measurement instruments and for a multidisciplinary collaboration.

Links between Evolution, Development, Human Anatomy, Pathology, and Medicine, with A Proposition of A Re-defined Anatomical Position and Notes on Constraints and Morphological "Imperfections".

PubMed

Diogo, Rui; Molnar, Julia

2016-06-01

Surprisingly the oldest formal discipline in medicine (anatomy) has not yet felt the full impact of evolutionary developmental biology. In medical anatomy courses and textbooks, the human body is still too often described as though it is a "perfect machine." In fact, the study of human anatomy predates evolutionary theory; therefore, many of its conventions continue to be outdated, making it difficult to study, understand, and treat the human body, and to compare it with that of other, nonbipedal animals, including other primates. Moreover, such an erroneous view of our anatomy as "perfect" can be used to fuel nonevolutionary ideologies such as intelligent design. In the section An Evolutionary and Developmental Approach to Human Anatomical Position of this paper, we propose the redefinition of the "human standard anatomical position" used in textbooks to be consistent with human evolutionary and developmental history. This redefined position also simplifies, for students and practitioners of the health professions, the study and learning of embryonic muscle groups (each group including muscles derived from the same/ontogenetically closely related primordium/primordia) and joint movements and highlights the topological correspondence between the upper and lower limbs. Section Evolutionary and Developmental Constraints, "Imperfections" and Sports Pathologies continues the theme by describing examples of apparently "illogical" characteristics of the human body that only make sense when one understands the developmental and evolutionary constraints that have accumulated over millions of years. We focus, in particular, on musculoskeletal functional problems and sports pathologies to emphasize the links with pathology and medicine. These examples demonstrate how incorporating evolutionary theory into anatomy education can be helpful for medical students, teachers, researchers, and physicians, as well as for anatomists, functional morphologists, and evolutionary and developmental biologists. © 2016 Wiley Periodicals, Inc.

Protein sectors: evolutionary units of three-dimensional structure

PubMed Central

Halabi, Najeeb; Rivoire, Olivier; Leibler, Stanislas; Ranganathan, Rama

2011-01-01

Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-independent groups of correlated amino acids that we term “protein sectors”. Each sector is physically connected in the tertiary structure, has a distinct functional role, and constitutes an independent mode of sequence divergence in the protein family. Functionally relevant sectors are evident in other protein families as well, suggesting that they may be general features of proteins. We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories. PMID:19703402

Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

PubMed Central

Zhang, Xian; Liu, Xueduan; Yang, Fei; Chen, Lv

2018-01-01

Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an ‘open’ pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation. PMID:29636744

[Charles Darwin and the problem of evolutionary progress].

PubMed

Iordanskiĭ, N N

2010-01-01

According to Ch. Darwin's evolutionary theory, evolutionary progress (interpreted as morpho-physiological progress or arogenesis in recent terminology) is one of logical results of natural selection. At the same time, natural selection does not hold any factors especially promoting evolutionary progress. Darwin emphasized that the pattern of evolutionary changes depends on organism nature more than on the pattern of environment changes. Arogenesis specificity is determined by organization of rigorous biological systems - integral organisms. Onward progressive development is determined by fundamental features of living organisms: metabolism and homeostasis. The concept of social Darwinism differs fundamentally from Darwin's ideas about the most important role of social instincts in progress of mankind. Competition and selection play secondary role in socio-cultural progress of human society.

An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease.

PubMed

Aoshiba, Kazutetsu; Tsuji, Takao; Itoh, Masayuki; Yamaguchi, Kazuhiro; Nakamura, Hiroyuki

2015-01-01

Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.

Biological causal links on physiological and evolutionary time scales.

PubMed

Karmon, Amit; Pilpel, Yitzhak

2016-04-26

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Relevance of East African Drill Cores to Human Evolution: the Case of the Olorgesailie Drilling Project

NASA Astrophysics Data System (ADS)

Potts, R.

2016-12-01

Drill cores reaching the local basement of the East African Rift were obtained in 2012 south of the Olorgesailie Basin, Kenya, 20 km from excavations that document key benchmarks in the origin of Homo sapiens. Sediments totaling 216 m were obtained from two drilling locations representing the past 1 million years. The cores were acquired to build a detailed environmental record spatially associated with the transition from Acheulean to Middle Stone Age technology and extensive turnover in mammalian species. The project seeks precise tests of how climate dynamics and tectonic events were linked with these transitions. Core lithology (A.K. Behrensmeyer), geochronology (A. Deino), diatoms (R.B. Owen), phytoliths (R. Kinyanjui), geochemistry (N. Rabideaux, D. Deocampo), among other indicators, show evidence of strong environmental variability in agreement with predicted high-eccentricity modulation of climate during the evolutionary transitions. Increase in hominin mobility, elaboration of symbolic behavior, and concurrent turnover in mammalian species indicating heightened adaptability to unpredictable ecosystems, point to a direct link between the evolutionary transitions and the landscape dynamics reflected in the Olorgesailie drill cores. For paleoanthropologists and Earth scientists, any link between evolutionary transitions and environmental dynamics requires robust evolutionary datasets pertinent to how selection, extinction, population divergence, and other evolutionary processes were impacted by the dynamics uncovered in drill core studies. Fossil and archeological data offer a rich source of data and of robust environment-evolution explanations that must be integrated into efforts by Earth scientists who seek to examine high-resolution climate records of human evolution. Paleoanthropological examples will illustrate the opportunities that exist for connecting evolutionary benchmarks to the data obtained from drilled African muds. Project members: R. Potts, A.K. Behrensmeyer, E. Beverly, K. Brady, J. Bright, E. Brown, J. Clark, A. Cohen, A. Deino, P. deMenocal, D. Deocampo, R. Dommain, J.T. Faith, J. King, R. Kinyanjui, N. Levin, J. Moerman, V. Muiruri, A. Noren, R.B. Owen, N. Rabideaux, R. Renaut, S. Rucina, J. Russell, J. Scott, M. Stockhecke, K. Uno

Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

Treesearch

Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

2012-01-01

Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

Characterization of the Bacteroides fragilis bfr Gene Product Identifies a Bacterial DPS-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily

PubMed Central

Gauss, George H.; Reott, Michael A.; Rocha, Edson R.; Young, Mark J.; Douglas, Trevor

2012-01-01

A factor contributing to the pathogenicity of Bacteroides fragilis, the most common anaerobic species isolated from clinical infections, is the bacterium's extreme aerotolerance, which allows survival in oxygenated tissues prior to anaerobic abscess formation. We investigated the role of the bacterioferritin-related (bfr) gene in the B. fragilis oxidative stress response. The bfr mRNA levels are increased in stationary phase or in response to O2 or iron. In addition, bfr null mutants exhibit reduced aerotolerance, and the bfr gene product protects DNA from hydroxyl radical cleavage in vitro. Crystallographic studies revealed a protein with a dodecameric structure and greater similarity to an archaeal DNA protection in starved cells (DPS)-like protein than to the 24-subunit bacterioferritins. Similarity to the DPS-like (DPSL) protein extends to the subunit and includes a pair of conserved cysteine residues juxtaposed to a buried dimetal binding site within the four-helix bundle. Compared to archaeal DPSLs, however, this bacterial DPSL protein contains several unique features, including a significantly different conformation in the C-terminal tail that alters the number and location of pores leading to the central cavity and a conserved metal binding site on the interior surface of the dodecamer. Combined, these characteristics confirm this new class of miniferritin in the bacterial domain, delineate the similarities and differences between bacterial DPSL proteins and their archaeal homologs, allow corrected annotations for B. fragilis bfr and other dpsl genes within the bacterial domain, and suggest an evolutionary link within the ferritin superfamily that connects dodecameric DPS to the (bacterio)ferritin 24-mer. PMID:22020642

The evolution of plant-insect mutualisms.

PubMed

Bronstein, Judith L; Alarcón, Ruben; Geber, Monica

2006-01-01

Mutualisms (cooperative interactions between species) have had a central role in the generation and maintenance of life on earth. Insects and plants are involved in diverse forms of mutualism. Here we review evolutionary features of three prominent insect-plant mutualisms: pollination, protection and seed dispersal. We focus on addressing five central phenomena: evolutionary origins and maintenance of mutualism; the evolution of mutualistic traits; the evolution of specialization and generalization; coevolutionary processes; and the existence of cheating. Several features uniting very diverse insect-plant mutualisms are identified and their evolutionary implications are discussed: the involvement of one mobile and one sedentary partner; natural selection on plant rewards; the existence of a continuum from specialization to generalization; and the ubiquity of cheating, particularly on the part of insects. Plant-insect mutualisms have apparently both arisen and been lost repeatedly. Many adaptive hypotheses have been proposed to explain these transitions, and it is unlikely that any one of them dominates across interactions differing so widely in natural history. Evolutionary theory has a potentially important, but as yet largely unfilled, role to play in explaining the origins, maintenance, breakdown and evolution of insect-plant mutualisms.

Neutral stability, drift, and the diversification of languages.

PubMed

Pawlowitsch, Christina; Mertikopoulos, Panayotis; Ritt, Nikolaus

2011-10-21

The diversification of languages is one of the most interesting facts about language that seek explanation from an evolutionary point of view. Conceptually the question is related to explaining mechanisms of speciation. An argument that prominently figures in evolutionary accounts of language diversification is that it serves the formation of group markers which help to enhance in-group cooperation. In this paper we use the theory of evolutionary games to show that language diversification on the level of the meaning of lexical items can come about in a perfectly cooperative world solely as a result of the effects of frequency-dependent selection. Importantly, our argument does not rely on some stipulated function of language diversification in some co-evolutionary process, but comes about as an endogenous feature of the model. The model that we propose is an evolutionary language game in the style of Nowak et al. (1999) [The evolutionary language game. J. Theor. Biol. 200, 147-162], which has been used to explain the rise of a signaling system or protolanguage from a prelinguistic environment. Our analysis focuses on the existence of neutrally stable polymorphisms in this model, where, on the level of the population, a signal can be used for more than one concept or a concept can be inferred by more than one signal. Specifically, such states cannot be invaded by a mutation for bidirectionality, that is, a mutation that tries to resolve the existing ambiguity by linking each concept to exactly one signal in a bijective way. However, such states are not resistant against drift between the selectively neutral variants that are present in such a state. Neutral drift can be a pathway for a mutation for bidirectionality that was blocked before but that finally will take over the population. Different directions of neutral drift open the door for a mutation for bidirectionality to appear on different resident types. This mechanism-which can be seen as a form of shifting balance-can explain why a word can acquire a different meaning in two languages that go back to the same common ancestral language, thereby contributing to the splitting of these two languages. Examples from currently spoken languages, for instance, English clean and its German cognate klein with the meaning of "small," are provided. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression.

PubMed

Jacobs, Arne; Hughes, Martin R; Robinson, Paige C; Adams, Colin E; Elmer, Kathryn R

2018-05-31

Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout ( Salmo trutta ) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation.

Neutral biogeography and the evolution of climatic niches.

PubMed

Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien

2014-05-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.

Neutral biogeography and the evolution of climatic niches

PubMed Central

Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien

2014-01-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191

Chronic sun damage and the perception of age, health and attractiveness.

PubMed

Matts, Paul J; Fink, Bernhard

2010-04-01

Young and healthy-looking skin is a feature that is universally admired and considered attractive among humans. However, as we age, skin condition deteriorates due to a variety of intrinsic and extrinsic factors determined not only by genetics and physiological health but also by behaviour and lifestyle choice. As regards the latter, cumulative, repeated exposure to solar ultraviolet radiation (UVR) is linked intrinsically to the induction of specific types of skin cancer and the expression of cutaneous damage markers responsible for the majority of the visible signs of skin ageing. Here we review empirical evidence for skin-specific effects of chronic UVR exposure and relate it to perception of visible skin condition. In contrast to other dermatological accounts, we stress an evolutionary psychology context in understanding the significance of age-related changes in visible skin condition in human social cognition and interaction. We suggest that the "marriage" of the scientific fields of skin biology and evolutionary psychology provides a modern, powerful framework for investigating the causes, mechanisms and perception of chronic sun damage of skin, as it explains the human obsession with a youthful and healthy appearance. Hence, it may be that these insights bring true emotional impetus to the adoption of sun protection strategies, which could conceivably impact skin cancer rates in coming years.

Niche construction theory: a practical guide for ecologists.

PubMed

Odling-Smee, John; Erwin, Douglas H; Palkovacs, Eric P; Feldman, Marcus W; Laland, Kevin N

2013-03-01

Niche construction theory (NCT) explicitly recognizes environmental modication by organisms ("niche construction") and their legacy overtime ("ecological inheritance") to be evolutionary processes in their own right. Here we illustrate how niche construction theory provides usedl conceptual tools and theoretical insights for integrating ecosystem ecology and evolutionary theory. We begin by briefly describing NCT, and illustrating how it deifers from conventional evolutionary approaches. We then distinguish between two aspects ofniche construction--environment alteration and subsequent evolution in response to constructed environments--equating the first of these with "ecosystem engineering." We describe some of the ecological and evolutionary impacts on ecosystems of niche construction, ecosystem engineering and ecological inheritance, and illustrate how these processes trigger ecological and evolutionary feedbacks and leave detectable ecological signatures that are open to investigation. FIinally, we provide a practical guide to how NCT could be deployed by ecologists and evolutionary biologists to aeplore ecoeoolutionay dynamics. We suggest that, by highlighting the ecological and evolutionay ramifications of changes that organisms bring about in ecosystems, NCT helps link ecosystem ecology to evolutionary biology, potentially leading to a deeper understanding of how ecosystems change over time.

Evoecotoxicology: Environmental Changes and Life Features Development during the Evolutionary Process—the Record of the Past at Developmental Stages of Living Organisms

PubMed Central

Herkovits, Jorge

2006-01-01

For most of evolutionary history, scientific understanding of the environment and life forms is extremely limited. In this commentary I discuss the hypothesis that ontogenetic features of living organisms can be considered biomarkers of coevolution between organisms and physicochemical agents during Earth’s history. I provide a new vision of evolution based on correlations between metabolic features and stage-dependent susceptibility of organisms to physicochemical agents with well-known environmental signatures. Thus, developmental features potentially reflect environmental changes during evolution. From this perspective, early multicellular life forms would have flourished in the anoxic Earth more than 2 billion years ago, which is at least 1.2 billion years in advance of available fossil evidence. The remarkable transition to aerobic metabolism in gastrula-stage embryos potentially reflects evolution toward tridermic organisms by 2 billion years ago. Noteworthy changes in embryonic resistance to physicochemical agents at different developmental stages that can be observed in living organisms potentially reflect the influence of environmental stress conditions during different periods of evolutionary history. Evoecotoxicology, as a multidisciplinary and transdisciplinary approach, can enhance our understanding of evolution, including the phylogenetic significance of differences in susceptibility/resistance to physicochemical agents in different organisms. PMID:16882515

Ecological opportunity and predator–prey interactions: linking eco-evolutionary processes and diversification in adaptive radiations

PubMed Central

2018-01-01

Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mechanistic understanding of the link between microevolutionary processes and macroevolutionary patterns is thus needed, especially in trophic communities. Here, we use a trait-based eco-evolutionary model to investigate the mechanisms linking competition, predation and adaptive radiations. By combining available micro-evolutionary theory and simulations of adaptive radiations we show that intraspecific competition is crucial for diversification as it induces disruptive selection, in particular in early phases of radiation. The diversification rate is however decreased in later phases owing to interspecific competition as niche availability, and population sizes are decreased. We provide new insight into how predation tends to have a negative effect on prey diversification through decreased population sizes, decreased disruptive selection and through the exclusion of prey from parts of niche space. The seemingly disparate effects of competition and predation on adaptive radiations, listed in the literature, may thus be acting and interacting in the same adaptive radiation at different relative strength as the radiation progresses. PMID:29514970

Applying ecological and evolutionary theory to cancer: a long and winding road.

PubMed

Thomas, Frédéric; Fisher, Daniel; Fort, Philippe; Marie, Jean-Pierre; Daoust, Simon; Roche, Benjamin; Grunau, Christoph; Cosseau, Céline; Mitta, Guillaume; Baghdiguian, Stephen; Rousset, François; Lassus, Patrice; Assenat, Eric; Grégoire, Damien; Missé, Dorothée; Lorz, Alexander; Billy, Frédérique; Vainchenker, William; Delhommeau, François; Koscielny, Serge; Itzykson, Raphael; Tang, Ruoping; Fava, Fanny; Ballesta, Annabelle; Lepoutre, Thomas; Krasinska, Liliana; Dulic, Vjekoslav; Raynaud, Peggy; Blache, Philippe; Quittau-Prevostel, Corinne; Vignal, Emmanuel; Trauchessec, Hélène; Perthame, Benoit; Clairambault, Jean; Volpert, Vitali; Solary, Eric; Hibner, Urszula; Hochberg, Michael E

2013-01-01

Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance to therapies). Historically, little attention has been placed on applications of evolutionary biology to understanding and controlling neoplastic progression and to prevent therapeutic failures. This is now beginning to change, and there is a growing international interest in the interface between cancer and evolutionary biology. The objective of this introduction is first to describe the basic ideas and concepts linking evolutionary biology to cancer. We then present four major fronts where the evolutionary perspective is most developed, namely laboratory and clinical models, mathematical models, databases, and techniques and assays. Finally, we discuss several of the most promising challenges and future prospects in this interdisciplinary research direction in the war against cancer.

Universality and predictability in molecular quantitative genetics.

PubMed

Nourmohammad, Armita; Held, Torsten; Lässig, Michael

2013-12-01

Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent developments in evolutionary theory and experiments that are expected to become building blocks of a quantitative genetics of molecular traits. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least partially unknown. We show that universal measurements can be used to infer selection on a quantitative trait, which determines its evolutionary mode of conservation or adaptation. Furthermore, universality is closely linked to predictability of trait evolution across lineages. We argue that universal trait statistics extends over a range of cellular scales and opens new avenues of quantitative evolutionary systems biology. Copyright © 2013. Published by Elsevier Ltd.

Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau.

PubMed

Zhao, Zhe; Li, Shuqiang

2017-11-01

Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region. Based on eight genes (6.5 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China origin for them. Most extant, widespread species belong to the southern (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to associate with either the Paleocene-Eocene Thermal Maximum or the hot period in early Eocene. Tibetan uplifting events influenced the current diversity patterns of coelotines. The origin of SCG lies outside of the Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked dispersal since the Late Eocene. Continuous orogenesis appears to have created localized vicariant events, which drove rapid radiation in SCG. North-central Tibet is the likely location of origin for NCG and many lineages likely experienced extinction owing to uplifting since early Oligocene. Their evolutionary histories correspond with recent geological evidence that high-elevation orographical features existed in the Tibetan region as early as 40-35 Ma. Our discoveries may be the first empirical evidence that links the evolution of organisms to the Eocene-Oligocene uplifting of the Tibetan Plateau. [Tibet; biogeography; ecology; molecular clock; diversification.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Variation in stem anatomical characteristics of Campanuloideae species in relation to evolutionary history and ecological preferences.

PubMed

Schweingruber, Fritz Hans; Ríha, Pavel; Doležal, Jiří

2014-01-01

The detailed knowledge of plant anatomical characters and their variation among closely related taxa is key to understanding their evolution and function. We examined anatomical variation in 46 herbaceous taxa from the subfamily Campanuloideae (Campanulaceae) to link this information with their phylogeny, ecology and comparative material of 56 woody tropical taxa from the subfamily Lobelioideae. The species studied covered major environmental gradients from Mediterranean to Arctic zones, allowing us to test hypotheses on the evolution of anatomical structure in relation to plant competitive ability and ecological preferences. To understand the evolution of anatomical diversity, we reconstructed the phylogeny of studied species from nucleotide sequences and examined the distribution of anatomical characters on the resulting phylogenetic tree. Redundancy analysis, with phylogenetic corrections, was used to separate the evolutionary inertia from the adaptation to the environment. A large anatomical diversity exists within the Campanuloideae. Traits connected with the quality of fibres were the most congruent with phylogeny, and the Rapunculus 2 ("phyteumoid") clade was especially distinguished by a number of characters (absence of fibres, pervasive parenchyma, type of rays) from two other clades (Campanula s. str. and Rapunculus 1) characterized by the dominance of fibres and the absence of parenchyma. Septate fibres are an exclusive trait in the Lobelioideae, separating it clearly from the Campanuloideae where annual rings, pervasive parenchyma and crystals in the phellem are characteristic features. Despite clear phylogenetic inertia in the anatomical features studied, the ecological attributes and plant height had a significant effect on anatomical divergence. From all three evolutionary clades, the taller species converged towards similar anatomical structure, characterized by a smaller number of early wood vessels of large diameter, thinner cell-walls and alternate intervessel pits, while the opposite trend was found in small Arctic and alpine taxa. This supports the existing generalization that narrower vessels allow plants to grow in colder places where they can avoid freezing-induced embolism, while taller plants have wider vessels to minimize hydraulic resistance with their greater path lengths.

Variation in Stem Anatomical Characteristics of Campanuloideae Species in Relation to Evolutionary History and Ecological Preferences

PubMed Central

Schweingruber, Fritz Hans; Říha, Pavel; Doležal, Jiří

2014-01-01

Background The detailed knowledge of plant anatomical characters and their variation among closely related taxa is key to understanding their evolution and function. We examined anatomical variation in 46 herbaceous taxa from the subfamily Campanuloideae (Campanulaceae) to link this information with their phylogeny, ecology and comparative material of 56 woody tropical taxa from the subfamily Lobelioideae. The species studied covered major environmental gradients from Mediterranean to Arctic zones, allowing us to test hypotheses on the evolution of anatomical structure in relation to plant competitive ability and ecological preferences. Methodology/Principal Findings To understand the evolution of anatomical diversity, we reconstructed the phylogeny of studied species from nucleotide sequences and examined the distribution of anatomical characters on the resulting phylogenetic tree. Redundancy analysis, with phylogenetic corrections, was used to separate the evolutionary inertia from the adaptation to the environment. A large anatomical diversity exists within the Campanuloideae. Traits connected with the quality of fibres were the most congruent with phylogeny, and the Rapunculus 2 (“phyteumoid”) clade was especially distinguished by a number of characters (absence of fibres, pervasive parenchyma, type of rays) from two other clades (Campanula s. str. and Rapunculus 1) characterized by the dominance of fibres and the absence of parenchyma. Septate fibres are an exclusive trait in the Lobelioideae, separating it clearly from the Campanuloideae where annual rings, pervasive parenchyma and crystals in the phellem are characteristic features. Conclusions/Significance Despite clear phylogenetic inertia in the anatomical features studied, the ecological attributes and plant height had a significant effect on anatomical divergence. From all three evolutionary clades, the taller species converged towards similar anatomical structure, characterized by a smaller number of early wood vessels of large diameter, thinner cell-walls and alternate intervessel pits, while the opposite trend was found in small Arctic and alpine taxa. This supports the existing generalization that narrower vessels allow plants to grow in colder places where they can avoid freezing-induced embolism, while taller plants have wider vessels to minimize hydraulic resistance with their greater path lengths. PMID:24586306

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

PubMed Central

Jin, Xiaoli; Ren, Jing; Nevo, Eviatar; Yin, Xuegui; Sun, Dongfa; Peng, Junhua

2017-01-01

NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses. PMID:28713414

Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association.

PubMed

Kingston, S E; Martino, P; Melendy, M; Reed, F A; Carlon, D B

2018-03-01

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here, we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells - like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a 'climate change' common garden, where we raised temperature by 3°C, decreased pH by 0.2 units and limited food supply by filtering out planktonic particles >5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170 000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2-10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of >90% when effective sample size is 900. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Evolutionary and mechanistic theories of aging.

PubMed

Hughes, Kimberly A; Reynolds, Rose M

2005-01-01

Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?

Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning.

PubMed

Davies, T Jonathan; Urban, Mark C; Rayfield, Bronwyn; Cadotte, Marc W; Peres-Neto, Pedro R

2016-09-01

Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity-ecosystem-function literature. © 2016 by the Ecological Society of America.

Self-adaptive MOEA feature selection for classification of bankruptcy prediction data.

PubMed

Gaspar-Cunha, A; Recio, G; Costa, L; Estébanez, C

2014-01-01

Bankruptcy prediction is a vast area of finance and accounting whose importance lies in the relevance for creditors and investors in evaluating the likelihood of getting into bankrupt. As companies become complex, they develop sophisticated schemes to hide their real situation. In turn, making an estimation of the credit risks associated with counterparts or predicting bankruptcy becomes harder. Evolutionary algorithms have shown to be an excellent tool to deal with complex problems in finances and economics where a large number of irrelevant features are involved. This paper provides a methodology for feature selection in classification of bankruptcy data sets using an evolutionary multiobjective approach that simultaneously minimise the number of features and maximise the classifier quality measure (e.g., accuracy). The proposed methodology makes use of self-adaptation by applying the feature selection algorithm while simultaneously optimising the parameters of the classifier used. The methodology was applied to four different sets of data. The obtained results showed the utility of using the self-adaptation of the classifier.

Self-Adaptive MOEA Feature Selection for Classification of Bankruptcy Prediction Data

PubMed Central

Gaspar-Cunha, A.; Recio, G.; Costa, L.; Estébanez, C.

2014-01-01

Bankruptcy prediction is a vast area of finance and accounting whose importance lies in the relevance for creditors and investors in evaluating the likelihood of getting into bankrupt. As companies become complex, they develop sophisticated schemes to hide their real situation. In turn, making an estimation of the credit risks associated with counterparts or predicting bankruptcy becomes harder. Evolutionary algorithms have shown to be an excellent tool to deal with complex problems in finances and economics where a large number of irrelevant features are involved. This paper provides a methodology for feature selection in classification of bankruptcy data sets using an evolutionary multiobjective approach that simultaneously minimise the number of features and maximise the classifier quality measure (e.g., accuracy). The proposed methodology makes use of self-adaptation by applying the feature selection algorithm while simultaneously optimising the parameters of the classifier used. The methodology was applied to four different sets of data. The obtained results showed the utility of using the self-adaptation of the classifier. PMID:24707201

Homologs of CD83 from elasmobranch and teleost fish.

PubMed

Ohta, Yuko; Landis, Eric; Boulay, Thomas; Phillips, Ruth B; Collet, Bertrand; Secombes, Chris J; Flajnik, Martin F; Hansen, John D

2004-10-01

Dendritic cells are one of the most important cell types connecting innate and adaptive immunity, but very little is known about their evolutionary origins. To begin to study dendritic cells from lower vertebrates, we isolated and characterized CD83 from the nurse shark (Ginglymostoma cirratum (Gici)) and rainbow trout (Oncorhynchus mykiss (Onmy)). The open reading frames for Gici-CD83 (194 aa) and Onmy-CD83 (218 aa) display approximately 28-32% identity to mammalian CD83 with the presence of two conserved N-linked glycosylation sites. Identical with mammalian CD83 genes, Gici-CD83 is composed of five exons including conservation of phase for the splice sites. Mammalian CD83 genes contain a split Ig superfamily V domain that represents a unique sequence feature for CD83 genes, a feature conserved in both Gici- and Onmy-CD83. Gici-CD83 and Onmy-CD83 are not linked to the MHC, an attribute shared with mouse but not human CD83. Gici-CD83 is expressed rather ubiquitously with highest levels in the epigonal tissue, a primary site for lymphopoiesis in the nurse shark, whereas Onmy-CD83 mRNA expression largely paralleled that of MHC class II but at lower levels. Finally, Onmy-CD83 gene expression is up-regulated in virus-infected trout, and the promoter is responsive to trout IFN regulatory factor-1. These results suggest that the role of CD83, an adhesion molecule for cell-mediated immunity, has been conserved over 450 million years of vertebrate evolution.

Beyond the pleistocene: using phylogeny and constraint to inform the evolutionary psychology of human mating.

PubMed

Eastwick, Paul W

2009-09-01

Evolutionary psychologists explore the adaptive function of traits and behaviors that characterize modern Homo sapiens. However, evolutionary psychologists have yet to incorporate the phylogenetic relationship between modern Homo sapiens and humans' hominid and pongid relatives (both living and extinct) into their theorizing. By considering the specific timing of evolutionary events and the role of evolutionary constraint, researchers using the phylogenetic approach can generate new predictions regarding mating phenomena and derive new explanations for existing evolutionary psychological findings. Especially useful is the concept of the adaptive workaround-an adaptation that manages the maladaptive elements of a pre-existing evolutionary constraint. The current review organizes 7 features of human mating into their phylogenetic context and presents evidence that 2 adaptive workarounds played a critical role as Homo sapiens's mating psychology evolved. These adaptive workarounds function in part to mute or refocus the effects of older, previously evolved adaptations and highlight the layered nature of humans' mating psychology. (c) 2009 APA, all rights reserved.

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

PubMed

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian T

2014-11-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Integrating instance selection, instance weighting, and feature weighting for nearest neighbor classifiers by coevolutionary algorithms.

PubMed

Derrac, Joaquín; Triguero, Isaac; Garcia, Salvador; Herrera, Francisco

2012-10-01

Cooperative coevolution is a successful trend of evolutionary computation which allows us to define partitions of the domain of a given problem, or to integrate several related techniques into one, by the use of evolutionary algorithms. It is possible to apply it to the development of advanced classification methods, which integrate several machine learning techniques into a single proposal. A novel approach integrating instance selection, instance weighting, and feature weighting into the framework of a coevolutionary model is presented in this paper. We compare it with a wide range of evolutionary and nonevolutionary related methods, in order to show the benefits of the employment of coevolution to apply the techniques considered simultaneously. The results obtained, contrasted through nonparametric statistical tests, show that our proposal outperforms other methods in the comparison, thus becoming a suitable tool in the task of enhancing the nearest neighbor classifier.

Mars: Lithospheric Flexure of the Tharsis Montes Volcanoes and the Evolutionary Relationship to Their Tectonic History

NASA Astrophysics Data System (ADS)

Chute, H.; Dombard, A. J.; Byrne, P. K.

2017-12-01

Lithospheric flexure associated with Arsia, Pavonis, and Ascraeus Montes has been previously studied to constrain the timeline and breadth of endogenic surface features surrounding these volcanoes. Here, we simulate the radial extent of two specific load-related features: annular graben and flank terraces. Detailed mapping of Ascraeus Mons (the youngest of the three volcanoes) showed a phase of compression of the edifice, forming the terraces and an annulus of graben immediately off the flanks, followed by a period of extension that formed additional graben superposed on the terraces on the lower flanks of the edifice. This transition from compression to extension on the lower flanks has been difficult to reconcile in mechanical models. We explore, with finite-element simulations, the effects of a thermal anomaly associated with an intrusive crustal underplate, which results in locally thinning the lithosphere (in contrast to past efforts that assumed a constant-thickness lithosphere). We find that it is primarily the horizontal extent of this thermal anomaly that governs how the lithosphere flexes under a volcano, as well as the transition from flank compression to a tight annulus of extensional stresses. Specifically, we propose that the structures on Ascraeus may be consistent with an early stage of volcanic growth accompanied by an underplate about the same width as the edifice that narrowed as volcanism waned, resulting in an inward migration of the extensional horizontal stresses from the surrounding plains onto the lower flanks. By linking the surface strains on the volcano with the volcano-tectonic evolution predicted by our flexure model, we can further constrain a more accurate timeline for the tectonic history of Ascraeus Mons. More broadly, because these tectonic structures are commonly observed, our results provide a general evolutionary model for large shield volcanoes on Mars.

Evolutionary Dynamics of the Gametologous CTNNB1 Gene on the Z and W Chromosomes of Snakes.

PubMed

Laopichienpong, Nararat; Muangmai, Narongrit; Chanhome, Lawan; Suntrarachun, Sunutcha; Twilprawat, Panupon; Peyachoknagul, Surin; Srikulnath, Kornsorn

2017-03-01

Snakes exhibit genotypic sex determination with female heterogamety (ZZ males and ZW females), and the state of sex chromosome differentiation also varies among lineages. To investigate the evolutionary history of homologous genes located in the nonrecombining region of differentiated sex chromosomes in snakes, partial sequences of the gametologous CTNNB1 gene were analyzed for 12 species belonging to henophid (Cylindrophiidae, Xenopeltidae, and Pythonidae) and caenophid snakes (Viperidae, Elapidae, and Colubridae). Nonsynonymous/synonymous substitution ratios (Ka/Ks) in coding sequences were low (Ka/Ks < 1) between CTNNB1Z and CTNNB1W, suggesting that these 2 genes may have similar functional properties. However, frequencies of intron sequence substitutions and insertion–deletions were higher in CTNNB1Z than CTNNB1W, suggesting that Z-linked sequences evolved faster than W-linked sequences. Molecular phylogeny based on both intron and exon sequences showed the presence of 2 major clades: 1) Z-linked sequences of Caenophidia and 2) W-linked sequences of Caenophidia clustered with Z-linked sequences of Henophidia, which suggests that the sequence divergence between CTNNB1Z and CTNNB1W in Caenophidia may have occurred by the cessation of recombination after the split from Henophidia.

Commentary on "The Evolutionary Origin of Female Orgasm" by M. Pavlicev and G. Wagner, 2016, J. Exp. Zool. (Mol. Dev. Evol.) 326(6):326-337.

PubMed

Komisaruk, Barry R

2016-12-01

Evidence is presented as an alternative to the authors' claims that in the course of evolution, a link between orgasm and ovulation has been lost in women, that evolutionary changes in clitoral anatomy underlie this loss, and that women's orgasm plays no significant role in reproduction. © 2016 Wiley Periodicals, Inc.

EvoluZion: A Computer Simulator for Teaching Genetic and Evolutionary Concepts

ERIC Educational Resources Information Center

Zurita, Adolfo R.

2017-01-01

EvoluZion is a forward-in-time genetic simulator developed in Java and designed to perform real time simulations on the evolutionary history of virtual organisms. These model organisms harbour a set of 13 genes that codify an equal number of phenotypic features. These genes change randomly during replication, and mutant genes can have null,…

Eco-Evolutionary Genomics of Chromosomal Inversions.

PubMed

Wellenreuther, Maren; Bernatchez, Louis

2018-05-03

Chromosomal inversions have long fascinated evolutionary biologists due to their suppression of recombination, which can protect co-adapted alleles. Emerging research documents that inversions are commonly linked to spectacular phenotypes and have a pervasive role in eco-evolutionary processes, from mating systems, social organisation, environmental adaptation, and reproductive isolation to speciation. Studies also reveal that inversions are taxonomically widespread, with many being old and large, and that balancing selection is commonly facilitating their maintenance. This challenges the traditional view that the role of balancing selection in maintaining variation is relatively minor. The ubiquitous importance of inversions in ecological and evolutionary processes suggests that structural variation should be better acknowledged and integrated in studies pertaining to the molecular basis of adaptation and speciation. Copyright © 2018 Elsevier Ltd. All rights reserved.

XtalOpt  version r9: An open-source evolutionary algorithm for crystal structure prediction

DOE PAGES

Falls, Zackary; Lonie, David C.; Avery, Patrick; ...

2015-10-23

This is a new version of XtalOpt, an evolutionary algorithm for crystal structure prediction available for download from the CPC library or the XtalOpt website, http://xtalopt.github.io. XtalOpt is published under the Gnu Public License (GPL), which is an open source license that is recognized by the Open Source Initiative. We have detailed the new version incorporates many bug-fixes and new features here and predict the crystal structure of a system from its stoichiometry alone, using evolutionary algorithms.

On suffering and sympathy: "Jude the Obscure," evolution, and ethics.

PubMed

Sumpter, Caroline

2011-01-01

This article links Thomas Hardy's exploration of sympathy in "Jude the Obscure" to contemporary scientific debates over moral evolution. Tracing the relationship between pessimism, progressivism, and determinism in Hardy's understanding of sympathy, it also considers Hardy's conception of the author as enlarger of 'social sympathies' - a position, I argue, that was shaped by Leslie Stephen's advocacy of novel writing as moral art. Considering Hardy's engagement with writings by Charles Darwin, T.H. Huxley, Herbert Spencer, and others, I explore the novel's participation in a debate about the evolutionary significance of sympathy and its implications for Hardy's understanding of moral agency. Hardy, I suggest, offered a stronger defence of morality based on biological determinism than Darwin, but this determinism was linked to an unexpected evolutionary optimism.

Occurrence of neanderthal features in mandibles from the Atapuerca-SH site.

PubMed

Rosas, A

2001-01-01

Analysis of variation and distribution of evolutionary novelties is meaningful in understanding evolutionary processes. The mandible, as a morphological complex, comprises a large number of derived Neanderthal features. The present study investigates whether the features usually considered as European lineage apomorphies evolved independently; the occurrence of these features is studied in the mandibles from the Sima de los Huesos (SH) site (Atapuerca, Spain). For comparative purposes, a large sample of Neanderthal mandibles as well as older fossil Homo specimens have been used for the study. Chi-square tests were employed to test for independence. The SH mandibles present a set of features that clearly show the basic architecture of the Neanderthal mandible. A highly significant association is detected in the variation of the position of the mental foramen, the lateral prominence, and the anterior marginal tubercle, as well as in the development of retromolar space. However, a much weaker association is detected in the features of the internal aspect of the mandible, with a few exceptions. Features of the external aspect of the mandible occur chronologically earlier than those observed in the internal aspect. The hypothesis that two distinct and consecutive morphological processes have driven the emergence of the European lineage throughout the Middle Pleistocene is proposed. A first transformation affects the mandible by means of backwards displacement of the structures located at the external aspect, as well as the position of the condyle. A second process would modify the features of the internal aspect of the mandible, in which the relief of the masseteric and pterygoid fossae are affected, in association with a spatial rearrangement of the corpus and ramus. Analyzed individually, some of the considered features may be questioned as Neanderthal apomorphies (Trinkaus,1993; Franciscus and Trinkaus, 995); however, the joint occurrence of many of them suggests that the complex is an evolutionary novelty. Copyright 2001 Wiley-Liss, Inc.

Making evolutionary biology a basic science for medicine

PubMed Central

Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

2010-01-01

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

PubMed

Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

2010-01-26

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

Dinosaurs, Chameleons, Humans, and Evo-Devo Path: Linking Étienne Geoffroy's Teratology, Waddington's Homeorhesis, Alberch's Logic of "Monsters," and Goldschmidt Hopeful "Monsters".

PubMed

Diogo, Rui; Guinard, Geoffrey; Diaz, Raul E

2017-05-01

Since the rise of evo-devo (evolutionary developmental biology) in the 1980s, few authors have attempted to combine the increasing knowledge obtained from the study of model organisms and human medicine with data from comparative anatomy and evolutionary biology in order to investigate the links between development, pathology, and macroevolution. Fortunately, this situation is slowly changing, with a renewed interest in evolutionary developmental pathology (evo-devo-path) in the past decades, as evidenced by the idea to publish this special, and very timely, issue on "Developmental Evolution in Biomedical Research." As all of us have recently been involved, independently, in works related in some way or another with evolution and developmental anomalies, we decided to join our different perspectives and backgrounds in the present contribution for this special issue. Specifically, we provide a brief historical account on the study of the links between evolution, development, and pathologies, followed by a review of the recent work done by each of us, and then by a general discussion on the broader developmental and macroevolutionary implications of our studies and works recently done by other authors. Our primary aims are to highlight the strength of studying developmental anomalies within an evolutionary framework to understand morphological diversity and disease by connecting the recent work done by us and others with the research done and broader ideas proposed by authors such as Étienne Geoffroy Saint-Hilaire, Waddington, Goldschmidt, Gould, and Per Alberch, among many others to pave the way for further and much needed work regarding abnormal development and macroevolution. © 2016 Wiley Periodicals, Inc.

Classification of motor imagery tasks for BCI with multiresolution analysis and multiobjective feature selection.

PubMed

Ortega, Julio; Asensio-Cubero, Javier; Gan, John Q; Ortiz, Andrés

2016-07-15

Brain-computer interfacing (BCI) applications based on the classification of electroencephalographic (EEG) signals require solving high-dimensional pattern classification problems with such a relatively small number of training patterns that curse of dimensionality problems usually arise. Multiresolution analysis (MRA) has useful properties for signal analysis in both temporal and spectral analysis, and has been broadly used in the BCI field. However, MRA usually increases the dimensionality of the input data. Therefore, some approaches to feature selection or feature dimensionality reduction should be considered for improving the performance of the MRA based BCI. This paper investigates feature selection in the MRA-based frameworks for BCI. Several wrapper approaches to evolutionary multiobjective feature selection are proposed with different structures of classifiers. They are evaluated by comparing with baseline methods using sparse representation of features or without feature selection. The statistical analysis, by applying the Kolmogorov-Smirnoff and Kruskal-Wallis tests to the means of the Kappa values evaluated by using the test patterns in each approach, has demonstrated some advantages of the proposed approaches. In comparison with the baseline MRA approach used in previous studies, the proposed evolutionary multiobjective feature selection approaches provide similar or even better classification performances, with significant reduction in the number of features that need to be computed.

Discovery radiomics via evolutionary deep radiomic sequencer discovery for pathologically proven lung cancer detection.

PubMed

Shafiee, Mohammad Javad; Chung, Audrey G; Khalvati, Farzad; Haider, Masoom A; Wong, Alexander

2017-10-01

While lung cancer is the second most diagnosed form of cancer in men and women, a sufficiently early diagnosis can be pivotal in patient survival rates. Imaging-based, or radiomics-driven, detection methods have been developed to aid diagnosticians, but largely rely on hand-crafted features that may not fully encapsulate the differences between cancerous and healthy tissue. Recently, the concept of discovery radiomics was introduced, where custom abstract features are discovered from readily available imaging data. We propose an evolutionary deep radiomic sequencer discovery approach based on evolutionary deep intelligence. Motivated by patient privacy concerns and the idea of operational artificial intelligence, the evolutionary deep radiomic sequencer discovery approach organically evolves increasingly more efficient deep radiomic sequencers that produce significantly more compact yet similarly descriptive radiomic sequences over multiple generations. As a result, this framework improves operational efficiency and enables diagnosis to be run locally at the radiologist's computer while maintaining detection accuracy. We evaluated the evolved deep radiomic sequencer (EDRS) discovered via the proposed evolutionary deep radiomic sequencer discovery framework against state-of-the-art radiomics-driven and discovery radiomics methods using clinical lung CT data with pathologically proven diagnostic data from the LIDC-IDRI dataset. The EDRS shows improved sensitivity (93.42%), specificity (82.39%), and diagnostic accuracy (88.78%) relative to previous radiomics approaches.

Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

PubMed Central

Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A.; Janke, Axel

2015-01-01

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. PMID:26019166

A single determinant dominates the rate of yeast protein evolution.

PubMed

Drummond, D Allan; Raval, Alpan; Wilke, Claus O

2006-02-01

A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we carry out the first combined analysis of seven predictors (gene expression level, dispensability, protein abundance, codon adaptation index, gene length, number of protein-protein interactions, and the gene's centrality in the interaction network) previously reported to have independent influences on protein evolutionary rates. Strikingly, our analysis reveals a single dominant variable linked to the number of translation events which explains 40-fold more variation in evolutionary rate than any other, suggesting that protein evolutionary rate has a single major determinant among the seven predictors. The dominant variable explains nearly half the variation in the rate of synonymous and protein evolution. We show that the two most commonly used methods to disentangle the determinants of evolutionary rate, partial correlation analysis and ordinary multivariate regression, produce misleading or spurious results when applied to noisy biological data. We overcome these difficulties by employing principal component regression, a multivariate regression of evolutionary rate against the principal components of the predictor variables. Our results support the hypothesis that translational selection governs the rate of synonymous and protein sequence evolution in yeast.

Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella

PubMed Central

Harms, Alexander; Segers, Francisca H.I.D.; Quebatte, Maxime; Mistl, Claudia; Manfredi, Pablo; Körner, Jonas; Chomel, Bruno B.; Kosoy, Michael; Maruyama, Soichi; Engel, Philipp

2017-01-01

The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation. PMID:28338931

Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization.

PubMed

Zhao, Pengju; Yu, Ying; Feng, Wen; Du, Heng; Yu, Jian; Kang, Huimin; Zheng, Xianrui; Wang, Zhiquan; Liu, George E; Ernst, Catherine W; Ran, Xueqin; Wang, Jiafu; Liu, Jian-Feng

2018-05-01

Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing. We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs. These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation.

PubMed

Rabosky, Daniel L; Santini, Francesco; Eastman, Jonathan; Smith, Stephen A; Sidlauskas, Brian; Chang, Jonathan; Alfaro, Michael E

2013-01-01

Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales.

Leaf Photosynthetic Rate of Tropical Ferns Is Evolutionarily Linked to Water Transport Capacity

PubMed Central

Cao, Kun-Fang; Hu, Hong; Zhang, Jiao-Lin

2014-01-01

Ferns usually have relatively lower photosynthetic potential than angiosperms. However, it is unclear whether low photosynthetic potential of ferns is linked to leaf water supply. We hypothesized that there is an evolutionary association of leaf water transport capacity with photosynthesis and stomatal density in ferns. In the present study, a series of functional traits relating to leaf anatomy, hydraulics and physiology were assessed in 19 terrestrial and 11 epiphytic ferns in a common garden, and analyzed by a comparative phylogenetics method. Compared with epiphytic ferns, terrestrial ferns had higher vein density (Dvein), stomatal density (SD), stomatal conductance (gs), and photosynthetic capacity (Amax), but lower values for lower epidermal thickness (LET) and leaf thickness (LT). Across species, all traits varied significantly, but only stomatal length (SL) showed strong phylogenetic conservatism. Amax was positively correlated with Dvein and gs with and without phylogenetic corrections. SD correlated positively with Amax, Dvein and gs, with the correlation between SD and Dvein being significant after phylogenetic correction. Leaf water content showed significant correlations with LET, LT, and mesophyll thickness. Our results provide evidence that Amax of the studied ferns is linked to leaf water transport capacity, and there was an evolutionary association between water supply and demand in ferns. These findings add new insights into the evolutionary correlations among traits involving carbon and water economy in ferns. PMID:24416265

Intelligence and Fitness: The Mediating Role of Educational Level.

PubMed

Međedović, Janko

2017-01-01

The evolutionary status of intelligence is not clear: It is positively related to various indicators of fitness but negatively to reproductive success as the most important fitness marker. In the present research, we explored the links between intelligence and three fitness indicators: number of children (short-term reproductive success), number of grandchildren (long-term reproductive success), and age at first birth. Participants were individuals in a postreproductive stage ( N = 191; mean age = 66.5 years). Intelligence had a positive correlation with short-term reproductive success and age at first birth but a negative correlation with long-term reproductive success. Participants' education turned out to be a significant mediator of the link between intelligence and criterion measures. The results showed that intelligence can elevate short-term reproductive success. Furthermore, individuals with higher intellectual abilities tended to delay reproduction, which negatively affected their long-term reproductive success. Education was revealed as a very important resource which affects the link between cognitive abilities and fitness, thus proving its evolutionary role in contemporary populations.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Selfish genetic elements, genetic conflict, and evolutionary innovation

PubMed Central

Werren, John H.

2011-01-01

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs. PMID:21690392

The Reciprocal Links between Evolutionary-Ecological Sciences and Environmental Ethics.

ERIC Educational Resources Information Center

Rozzi, Ricardo

1999-01-01

Illustrates the reciprocal relationships between the sciences and environmental ethics by examining the Darwinian theory of evolution and discussing its implications for ecologists and ethicists. (CCM)

Evolutionary Algorithm Based Feature Optimization for Multi-Channel EEG Classification.

PubMed

Wang, Yubo; Veluvolu, Kalyana C

2017-01-01

The most BCI systems that rely on EEG signals employ Fourier based methods for time-frequency decomposition for feature extraction. The band-limited multiple Fourier linear combiner is well-suited for such band-limited signals due to its real-time applicability. Despite the improved performance of these techniques in two channel settings, its application in multiple-channel EEG is not straightforward and challenging. As more channels are available, a spatial filter will be required to eliminate the noise and preserve the required useful information. Moreover, multiple-channel EEG also adds the high dimensionality to the frequency feature space. Feature selection will be required to stabilize the performance of the classifier. In this paper, we develop a new method based on Evolutionary Algorithm (EA) to solve these two problems simultaneously. The real-valued EA encodes both the spatial filter estimates and the feature selection into its solution and optimizes it with respect to the classification error. Three Fourier based designs are tested in this paper. Our results show that the combination of Fourier based method with covariance matrix adaptation evolution strategy (CMA-ES) has the best overall performance.

Supercooperation in evolutionary games on correlated weighted networks.

PubMed

Buesser, Pierre; Tomassini, Marco

2012-01-01

In this work we study the behavior of classical two-person, two-strategies evolutionary games on a class of weighted networks derived from Barabási-Albert and random scale-free unweighted graphs. Using customary imitative dynamics, our numerical simulation results show that the presence of link weights that are correlated in a particular manner with the degree of the link end points leads to unprecedented levels of cooperation in the whole games' phase space, well above those found for the corresponding unweighted complex networks. We provide intuitive explanations for this favorable behavior by transforming the weighted networks into unweighted ones with particular topological properties. The resulting structures help us to understand why cooperation can thrive and also give ideas as to how such supercooperative networks might be built.

Item Feature Effects in Evolution Assessment

ERIC Educational Resources Information Center

Nehm, Ross H.; Ha, Minsu

2011-01-01

Despite concerted efforts by science educators to understand patterns of evolutionary reasoning in science students and teachers, the vast majority of evolution education studies have failed to carefully consider or control for item feature effects in knowledge measurement. Our study explores whether robust contextualization patterns emerge within…

Is the political animal politically ignorant? Applying evolutionary psychology to the study of political attitudes.

PubMed

Petersen, Michael Bang; Aarøe, Lene

2012-12-20

As evidenced by research in evolutionary psychology, humans have evolved sophisticated psychological mechanisms tailored to solve enduring adaptive problems of social life. Many of these social problems are political in nature and relate to the distribution of costs and benefits within and between groups. In that sense, evolutionary psychology suggests that humans are, by nature, political animals. By implication, a straightforward application of evolutionary psychology to the study of public opinion seems to entail that modern individuals find politics intrinsically interesting. Yet, as documented by more than fifty years of research in political science, people lack knowledge of basic features of the political process and the ability to form consistent political attitudes. By reviewing and integrating research in evolutionary psychology and public opinion, we describe (1) why modern mass politics often fail to activate evolved mechanisms and (2) the conditions in which these mechanisms are in fact triggered.

Evolutionary disarmament in interspecific competition.

PubMed

Kisdi, E; Geritz, S A

2001-12-22

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

Evolutionary disarmament in interspecific competition.

PubMed Central

Kisdi, E.; Geritz, S. A.

2001-01-01

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races. PMID:11749715

Woese on the received view of evolution.

PubMed

Sarkar, Sahotra

2014-01-01

As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing: (1) according to Woese's scenario of communal evolution during life's earliest phase (roughly, the first billion years of life on Earth), well-defined biological individuals (and, thus, individual lineages) did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. The extent to which this will be necessary will depend on whether Woese's scenario of collective early evolution is correct.

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

Feature Selection for Evolutionary Commercial-off-the-Shelf Software: Studies Focusing on Time-to-Market, Innovation and Hedonic-Utilitarian Trade-Offs

ERIC Educational Resources Information Center

Kakar, Adarsh Kumar

2013-01-01

Feature selection is one of the most important decisions made by product managers. This three article study investigates the concepts, tools and techniques for making trade-off decisions of introducing new features in evolving Commercial-Off-The-Shelf (COTS) software products. The first article investigates the efficacy of various feature…

Designing from minimum to optimum functionality

NASA Astrophysics Data System (ADS)

Bannova, Olga; Bell, Larry

2011-04-01

This paper discusses a multifaceted strategy to link NASA Minimal Functionality Habitable Element (MFHE) requirements to a compatible growth plan; leading forward to evolutionary, deployable habitats including outpost development stages. The discussion begins by reviewing fundamental geometric features inherent in small scale, vertical and horizontal, pressurized module configuration options to characterize applicability to meet stringent MFHE constraints. A proposed scenario to incorporate a vertical core MFHE concept into an expanded architecture to provide continuity of structural form and a logical path from "minimum" to "optimum" design of a habitable module. The paper describes how habitation and logistics accommodations could be pre-integrated into a common Hab/Log Module that serves both habitation and logistics functions. This is offered as a means to reduce unnecessary redundant development costs and to avoid EVA-intensive on-site adaptation and retrofitting requirements for augmented crew capacity. An evolutionary version of the hard shell Hab/Log design would have an expandable middle section to afford larger living and working accommodations. In conclusion, the paper illustrates that a number of cargo missions referenced for NASA's 4.0.0 Lunar Campaign Scenario could be eliminated altogether to expedite progress and reduce budgets. The plan concludes with a vertical growth geometry that provides versatile and efficient site development opportunities using a combination of hard Hab/Log modules and a hybrid expandable "CLAM" (Crew Lunar Accommodations Module) element.

Emergence and evolution of Santa Maria Island (Azores)—The conundrum of uplifted islands revisited

USGS Publications Warehouse

Ramalho, Ricardo; Helffrich, George; Madeira, Jose; Cosca, Michael A.; Thomas, Christine; Quartau, Rui; Hipolito, Ana; Rovere, Alessio; Hearty, Paul; Avila, Sergio

2017-01-01

The growth and decay of ocean-island volcanoes are intrinsically linked to vertical movements. While the causes for subsidence are better understood, uplift mechanisms remain enigmatic. Santa Maria Island in the Azores Archipelago is an ocean-island volcano resting on top of young lithosphere, barely 480 km away from the Mid-Atlantic Ridge. Like most other Azorean islands, Santa Maria should be experiencing subsidence. Yet, several features indicate an uplift trend instead. In this paper, we reconstruct the evolutionary history of Santa Maria with respect to the timing and magnitude of its vertical movements, using detailed field work and 40Ar/39Ar geochronology. Our investigations revealed a complex evolutionary history spanning ∼6 m.y., with subsidence up to ca. 3.5 Ma followed by uplift extending to the present day. The fact that an island located in young lithosphere experienced a pronounced uplift trend is remarkable and raises important questions concerning possible uplift mechanisms. Localized uplift in response to the tectonic regime affecting the southeastern tip of the Azores Plateau is unlikely, since the area is under transtension. Our analysis shows that the only viable mechanism able to explain the uplift is crustal thickening by basal intrusions, suggesting that intrusive processes play a significant role even on islands standing on young lithosphere, such as in the Azores.

Surfactant Lipids at the Host-Environment Interface. Metabolic Sensors, Suppressors, and Effectors of Inflammatory Lung Disease.

PubMed

Fessler, Michael B; Summer, Ross S

2016-05-01

The lipid composition of pulmonary surfactant is unlike that of any other body fluid. This extracellular lipid reservoir is also uniquely susceptible by virtue of its direct and continuous exposure to environmental oxidants, inflammatory agents, and pathogens. Historically, the greatest attention has been focused on those biophysical features of surfactant that serve to reduce surface tension at the air-liquid interface. More recently, surfactant lipids have also been recognized as bioactive molecules that maintain immune quiescence in the lung but can also be remodeled by the inhaled environment into neolipids that mediate key roles in inflammation, immunity, and fibrosis. This review focuses on the roles in inflammatory and infectious lung disease of two classes of native surfactant lipids, glycerophospholipids and sterols, and their corresponding oxidized species, oxidized glycerophospholipids and oxysterols. We highlight evidence that surfactant composition is sensitive to circulating lipoproteins and that the lipid milieu of the alveolus should thus be recognized as susceptible to diet and common systemic metabolic disorders. We also discuss intriguing evidence suggesting that oxidized surfactant lipids may represent an evolutionary link between immunity and tissue homeostasis that arose in the primordial lung. Taken together, the emerging picture is one in which the unique environmental susceptibility of the lung, together with its unique extracellular lipid requirements, may have made this organ both an evolutionary hub and an engine for lipid-immune cross-talk.

Primate vocal communication: a useful tool for understanding human speech and language evolution?

PubMed

Fedurek, Pawel; Slocombe, Katie E

2011-04-01

Language is a uniquely human trait, and questions of how and why it evolved have been intriguing scientists for years. Nonhuman primates (primates) are our closest living relatives, and their behavior can be used to estimate the capacities of our extinct ancestors. As humans and many primate species rely on vocalizations as their primary mode of communication, the vocal behavior of primates has been an obvious target for studies investigating the evolutionary roots of human speech and language. By studying the similarities and differences between human and primate vocalizations, comparative research has the potential to clarify the evolutionary processes that shaped human speech and language. This review examines some of the seminal and recent studies that contribute to our knowledge regarding the link between primate calls and human language and speech. We focus on three main aspects of primate vocal behavior: functional reference, call combinations, and vocal learning. Studies in these areas indicate that despite important differences, primate vocal communication exhibits some key features characterizing human language. They also indicate, however, that some critical aspects of speech, such as vocal plasticity, are not shared with our primate cousins. We conclude that comparative research on primate vocal behavior is a very promising tool for deepening our understanding of the evolution of human speech and language, but much is still to be done as many aspects of monkey and ape vocalizations remain largely unexplored.

Plant endemism in the Sierras of Córdoba and San Luis (Argentina): understanding links between phylogeny and regional biogeographical patterns.

PubMed

Chiapella, Jorge O; Demaio, Pablo H

2015-01-01

We compiled a checklist with all known endemic plants occurring in the Sierras of Córdoba and San Luis, an isolated mountainous range located in central Argentina. In order to obtain a better understanding of the evolutionary history, relationships and age of the regional flora, we gathered basic information on the biogeographical and floristic affinities of the endemics, and documented the inclusion of each taxon in molecular phylogenies. We listed 89 taxa (including 69 species and 20 infraspecific taxa) belonging to 53 genera and 29 families. The endemics are not distributed evenly, being more abundant in the lower than in the middle and upper vegetation belts. Thirty-two genera (60.3%) have been included in phylogenetic analyses, but only ten (18.8%) included local endemic taxa. A total of 28 endemic taxa of the Sierras CSL have a clear relationship with a widespread species of the same genus, or with one found close to the area. Available phylogenies for some taxa show divergence times between 7.0 - 1.8 Ma; all endemic taxa are most probably neoendemics sensu Stebbins and Major. Our analysis was specifically aimed at a particular geographic area, but the approach of analyzing phylogenetic patterns together with floristic or biogeographical relationships of the endemic taxa of an area, delimited by clear geomorphological features, could reveal evolutionary trends shaping the area.

Molecular Determinants of Cephalopod Muscles and Their Implication in Muscle Regeneration

PubMed Central

Zullo, Letizia; Fossati, Sara M.; Imperadore, Pamela; Nödl, Marie-Therese

2017-01-01

The ability to regenerate whole-body structures has been studied for many decades and is of particular interest for stem cell research due to its therapeutic potential. Several vertebrate and invertebrate species have been used as model systems to study pathways involved in regeneration in the past. Among invertebrates, cephalopods are considered as highly evolved organisms, which exhibit elaborate behavioral characteristics when compared to other mollusks including active predation, extraordinary manipulation, and learning abilities. These are enabled by a complex nervous system and a number of adaptations of their body plan, which were acquired over evolutionary time. Some of these novel features show similarities to structures present in vertebrates and seem to have evolved through a convergent evolutionary process. Octopus vulgaris (the common octopus) is a representative of modern cephalopods and is characterized by a sophisticated motor and sensory system as well as highly developed cognitive capabilities. Due to its phylogenetic position and its high regenerative power the octopus has become of increasing interest for studies on regenerative processes. In this paper we provide an overview over the current knowledge of cephalopod muscle types and structures and present a possible link between these characteristics and their high regenerative potential. This may help identify conserved molecular pathways underlying regeneration in invertebrate and vertebrate animal species as well as discover new leads for targeted tissue treatments in humans. PMID:28555185

Voltage-Gated Sodium Channels: Evolutionary History and Distinctive Sequence Features.

PubMed

Kasimova, M A; Granata, D; Carnevale, V

2016-01-01

Voltage-gated sodium channels (Nav) are responsible for the rising phase of the action potential. Their role in electrical signal transmission is so relevant that their emergence is believed to be one of the crucial factors enabling development of nervous system. The presence of voltage-gated sodium-selective channels in bacteria (BacNav) has raised questions concerning the evolutionary history of the ones in animals. Here we review some of the milestones in the field of Nav phylogenetic analysis and discuss some of the most important sequence features that distinguish these channels from voltage-gated potassium channels and transient receptor potential channels. Copyright © 2016 Elsevier Inc. All rights reserved.

Constructing phylogenetic trees using interacting pathways.

PubMed

Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.

Stellar Evolutionary Effects on the Abundances of PAH and SN-Condensed Dust in Galaxies

NASA Technical Reports Server (NTRS)

Dwek, Eliahu

2007-01-01

Spectral and photometric observations of nearby galaxies show a correlation between the strength of their mid-IR aromatic features, attributed to PAH molecules, and their metal abundance, leading to a deficiency of these features in low-metallicity galaxies. We suggest that the observed correlation represents a trend of PAH abundance with galactic age, reflecting the delayed injection of carbon dust into the ISM by AGB stars in the final post-AGB phase of their evolution. We also show that larger dust particles giving rise to the far-IR emission follow a distinct evolutionary trend closely related to the injection of dust by massive stars into the ISM.

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

PubMed Central

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

A neuropsychological perspective on the link between language and praxis in modern humans

PubMed Central

Roby-Brami, Agnes; Hermsdörfer, Joachim; Roy, Alice C.; Jacobs, Stéphane

2012-01-01

Hypotheses about the emergence of human cognitive abilities postulate strong evolutionary links between language and praxis, including the possibility that language was originally gestural. The present review considers functional and neuroanatomical links between language and praxis in brain-damaged patients with aphasia and/or apraxia. The neural systems supporting these functions are predominantly located in the left hemisphere. There are many parallels between action and language for recognition, imitation and gestural communication suggesting that they rely partially on large, common networks, differentially recruited depending on the nature of the task. However, this relationship is not unequivocal and the production and understanding of gestural communication are dependent on the context in apraxic patients and remains to be clarified in aphasic patients. The phonological, semantic and syntactic levels of language seem to share some common cognitive resources with the praxic system. In conclusion, neuropsychological observations do not allow support or rejection of the hypothesis that gestural communication may have constituted an evolutionary link between tool use and language. Rather they suggest that the complexity of human behaviour is based on large interconnected networks and on the evolution of specific properties within strategic areas of the left cerebral hemisphere. PMID:22106433

Evolution and Production of Calcareous Nannoplankton During the Cretaceous as Proxies of LIP-induced Oceanic Fertilization, Acidification and Anoxia

NASA Astrophysics Data System (ADS)

Erba, E.; Bottini, C.; Tiraboschi, D.

2008-12-01

Through the Phanerozoic, biota have been intimately linked to Earth's degassing inducing major changes in composition and structure of the ocean-atmosphere system. Emplacement of large igneous provinces (LIPs) has been the primary natural source of atmCO2 with dramatic consequences on climate and ecosystems. During the mid-Cretaceous the Ontong Java-Manihiki and Caribbean Plateaus LIPs are recognized as responsible of pCO2 as high as 2000 ppm. Coeval biocalcification crises occurred in pelagic and neritic settings, suggesting a causal link between high concentrations of carbon dioxide and drops in benthic and planktonic calcifiers' efficiency. Within the oceanic biosphere, calcareous nannoplankton play a key-role as: (1) is widespread and consists of cosmopolitan and endemic taxa; (2) has a 220 My-long evolutionary history; (3) is one the most effective calcite producers; (4) is relevant for the C cycle; (5) is extremely sensitive to environmental variations. Diversity pulses of Cretaceous calcareous nannoplankton are grossly coeval with LIP construction, climate and sea-level changes, variations in ocean structure and composition, suggesting that evolutionary patterns are closely linked to environmental modifications. We explored time-intervals of LIP formation marked by nannoplankton adaptation/evolution, quantifying evolutionary rates, species richness, abundance, calcite production and morphometry. High-resolution investigations of the initial phase of both early Aptian oceanic anoxic event (OAE) 1a and latest Cenomanian OAE 2 pointed out major evolutionary changes, decreases in heavily calcified nannoliths and occurrence of dwarf coccoliths. Nannoplankton calcification crises and dwarfism is here interpreted as forced by rapidly increasing pCO2 during formation of the Ontong Java-Maniniki and Caribbean Plateaus. Alternatively or concurrently, calcification crash and dwarfism might result from enhanced fertility associated to OAE1a and OAE2 regardless of ocean alkalinity. However, such global nutrification episodes must be linked as well to LIP construction via supply of biolimiting metals. Contrary to common reasoning, we stress the fact that emplacement of Cretaceous LIPs did not cause extinctions among calcareous nannoplankton.

Structure of N-linked oligosaccharides attached to chlorovirus PBCV-1 major capsid protein reveals unusual class of complex N-glycans

PubMed Central

De Castro, Cristina; Molinaro, Antonio; Piacente, Francesco; Gurnon, James R.; Sturiale, Luisa; Palmigiano, Angelo; Lanzetta, Rosa; Parrilli, Michelangelo; Garozzo, Domenico; Tonetti, Michela G.; Van Etten, James L.

2013-01-01

The major capsid protein Vp54 from the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains four Asn-linked glycans. The structure of the four N-linked oligosaccharides and the type of substitution at each glycosylation site was determined by chemical, spectroscopic, and spectrometric analyses. Vp54 glycosylation is unusual in many ways, including: (i) unlike most viruses, PBCV-1 encodes most, if not all, of the machinery to glycosylate its major capsid protein; (ii) the glycans are attached to the protein by a β-glucose linkage; (iii) the Asn-linked glycans are not located in a typical N-X-(T/S) consensus site; and (iv) the process probably occurs in the cytoplasm. The four glycoforms share a common core structure, and the differences are related to the nonstoichiometric presence of two monosaccharides. The most abundant glycoform consists of nine neutral monosaccharide residues, organized in a highly branched fashion. Among the most distinctive features of the glycoforms are (i) a dimethylated rhamnose as the capping residue of the main chain, (ii) a hyperbranched fucose unit, and (iii) two rhamnose residues with opposite absolute configurations. These glycoforms differ from what has been reported so far in the three domains of life. Considering that chloroviruses and other members of the family Phycodnaviridae may have a long evolutionary history, we suggest that the chlorovirus glycosylation pathway is ancient, possibly existing before the development of the endoplasmic reticulum and Golgi pathway, and involves still unexplored mechanisms. PMID:23918378

Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

PubMed

Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A; Janke, Axel

2015-05-27

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Historical change and evolutionary theory.

PubMed

Masters, Roger D

2007-09-01

Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological systems are constantly transformed by human technology and social behavior, multilevel evolutionary processes can explain two central features of human history: the rise, transformations, and ultimate fall of centralized governments (the "stuff" of history); and the biological uniqueness of Homo sapiens as the mammalian species that colonized--and became top carnivore--in virtually every habitable environment on the earth's surface. Once scholars admit the necessity of linking processes of natural selection with human transformations of the natural world, it will seem anomalous that it has taken so long to integrate Darwinian biology and the social sciences.

Allometry and Interspecific Differences in the Facial Cranium of Two Closely Related Macaque Species

PubMed Central

Ito, Tsuyoshi; Nishimura, Takeshi; Takai, Masanaru

2011-01-01

Interpreting evolutionary history of macaque monkeys from fossil evidence is difficult, because their evolutionary fluctuations in body size might have removed or formed important morphological features differently in each lineage. We employed geometric morphometrics to explore allometric trajectories of craniofacial shape in two closely related species, Macaca fascicularis and M. fuscata. These two species exhibit a single shared allometric trajectory in superoinferior deflection of the anterior face, indicating that the differences in this feature can be explained by size variation. In contrast, two parallel trajectories are demonstrated in craniofacial protrusion, indicating that even if they are comparable in size, M. fuscata has a higher and shorter face than M. fascicularis. The degree of facial protrusion is most likely a critical feature for phyletic evaluation in the fascicularis group. Such analyses in various macaques would help to resolve controversies regarding phyletic interpretations of fossil macaques. PMID:22567301

Extended evolution: A conceptual framework for integrating regulatory networks and niche construction

PubMed Central

Renn, Jürgen

2015-01-01

ABSTRACT This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path‐dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 565–577, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26097188

Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

PubMed

Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

2016-06-01

Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

Predicting missing links and identifying spurious links via likelihood analysis

NASA Astrophysics Data System (ADS)

Pan, Liming; Zhou, Tao; Lü, Linyuan; Hu, Chin-Kun

2016-03-01

Real network data is often incomplete and noisy, where link prediction algorithms and spurious link identification algorithms can be applied. Thus far, it lacks a general method to transform network organizing mechanisms to link prediction algorithms. Here we use an algorithmic framework where a network’s probability is calculated according to a predefined structural Hamiltonian that takes into account the network organizing principles, and a non-observed link is scored by the conditional probability of adding the link to the observed network. Extensive numerical simulations show that the proposed algorithm has remarkably higher accuracy than the state-of-the-art methods in uncovering missing links and identifying spurious links in many complex biological and social networks. Such method also finds applications in exploring the underlying network evolutionary mechanisms.

Predicting missing links and identifying spurious links via likelihood analysis

PubMed Central

Pan, Liming; Zhou, Tao; Lü, Linyuan; Hu, Chin-Kun

2016-01-01

Real network data is often incomplete and noisy, where link prediction algorithms and spurious link identification algorithms can be applied. Thus far, it lacks a general method to transform network organizing mechanisms to link prediction algorithms. Here we use an algorithmic framework where a network’s probability is calculated according to a predefined structural Hamiltonian that takes into account the network organizing principles, and a non-observed link is scored by the conditional probability of adding the link to the observed network. Extensive numerical simulations show that the proposed algorithm has remarkably higher accuracy than the state-of-the-art methods in uncovering missing links and identifying spurious links in many complex biological and social networks. Such method also finds applications in exploring the underlying network evolutionary mechanisms. PMID:26961965

Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods

PubMed Central

Valavanis, Ioannis; Pilalis, Eleftherios; Georgiadis, Panagiotis; Kyrtopoulos, Soterios; Chatziioannou, Aristotelis

2015-01-01

DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO) tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies. PMID:27600245

Image-Guided Rendering with an Evolutionary Algorithm Based on Cloud Model

PubMed Central

2018-01-01

The process of creating nonphotorealistic rendering images and animations can be enjoyable if a useful method is involved. We use an evolutionary algorithm to generate painterly styles of images. Given an input image as the reference target, a cloud model-based evolutionary algorithm that will rerender the target image with nonphotorealistic effects is evolved. The resulting animations have an interesting characteristic in which the target slowly emerges from a set of strokes. A number of experiments are performed, as well as visual comparisons, quantitative comparisons, and user studies. The average scores in normalized feature similarity of standard pixel-wise peak signal-to-noise ratio, mean structural similarity, feature similarity, and gradient similarity based metric are 0.486, 0.628, 0.579, and 0.640, respectively. The average scores in normalized aesthetic measures of Benford's law, fractal dimension, global contrast factor, and Shannon's entropy are 0.630, 0.397, 0.418, and 0.708, respectively. Compared with those of similar method, the average score of the proposed method, except peak signal-to-noise ratio, is higher by approximately 10%. The results suggest that the proposed method can generate appealing images and animations with different styles by choosing different strokes, and it would inspire graphic designers who may be interested in computer-based evolutionary art. PMID:29805440

Some Features of Human Adolescence Viewed in Evolutionary Perspective.

ERIC Educational Resources Information Center

Weisfeld, G. E.; Berger, J. M.

1983-01-01

Focuses on some apparently evolved features of human adolescence and their possible functions, including the pubertal growth spurt, sexual size dimorphism and bimaturism, the greater aggressiveness of males, heightened concern with one's social standing and the factors affecting it, intergenerational friction, same-sex aggregations and solidarity,…

Evolutionary heritage influences Amazon tree ecology.

PubMed

Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R

2016-12-14

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.

Evolutionary heritage influences Amazon tree ecology

PubMed Central

Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.

2016-01-01

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517

Exploring the evolutionary mechanism of complex supply chain systems using evolving hypergraphs

NASA Astrophysics Data System (ADS)

Suo, Qi; Guo, Jin-Li; Sun, Shiwei; Liu, Han

2018-01-01

A new evolutionary model is proposed to describe the characteristics and evolution pattern of supply chain systems using evolving hypergraphs, in which nodes represent enterprise entities while hyperedges represent the relationships among diverse trades. The nodes arrive at the system in accordance with a Poisson process, with the evolving process incorporating the addition of new nodes, linking of old nodes, and rewiring of links. Grounded in the Poisson process theory and continuum theory, the stationary average hyperdegree distribution is shown to follow a shifted power law (SPL), and the theoretical predictions are consistent with the results of numerical simulations. Testing the impact of parameters on the model yields a positive correlation between hyperdegree and degree. The model also uncovers macro characteristics of the relationships among enterprises due to the microscopic interactions among individuals.

Evolutionary rescue: linking theory for conservation and medicine.

PubMed

Alexander, Helen K; Martin, Guillaume; Martin, Oliver Y; Bonhoeffer, Sebastian

2014-12-01

Evolutionary responses that rescue populations from extinction when drastic environmental changes occur can be friend or foe. The field of conservation biology is concerned with the survival of species in deteriorating global habitats. In medicine, in contrast, infected patients are treated with chemotherapeutic interventions, but drug resistance can compromise eradication of pathogens. These contrasting biological systems and goals have created two quite separate research communities, despite addressing the same central question of whether populations will decline to extinction or be rescued through evolution. We argue that closer integration of the two fields, especially of theoretical understanding, would yield new insights and accelerate progress on these applied problems. Here, we overview and link mathematical modelling approaches in these fields, suggest specific areas with potential for fruitful exchange, and discuss common ideas and issues for empirical testing and prediction.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification.

PubMed

Badyaev, Alexander V; Morrison, Erin S; Belloni, Virginia; Sanderson, Michael J

2015-08-20

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness - the ability to synthesize the same carotenoid from an additional dietary starting point. We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage's metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration. The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

PubMed Central

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Pär K.

2016-01-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. PMID:26721855

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Causes and consequences of coagulation activation in sepsis: an evolutionary medicine perspective.

PubMed

Fiusa, Maiara Marx Luz; Carvalho-Filho, Marco Antonio; Annichino-Bizzacchi, Joyce M; De Paula, Erich V

2015-05-06

Coagulation and innate immunity have been linked together for at least 450 million years of evolution. Sepsis, one of the world's leading causes of death, is probably the condition in which this evolutionary link is more evident. However, the biological and the clinical relevance of this association have only recently gained the attention of the scientific community. During sepsis, the host response to a pathogen is invariably associated with coagulation activation. For several years, coagulation activation has been solely regarded as a mechanism of tissue damage, a concept that led to several clinical trials of anticoagulant agents for sepsis. More recently, this paradigm has been challenged by the failure of these clinical trials, and by a growing bulk of evidence supporting the concept that coagulation activation is beneficial for pathogen clearance. In this article we discuss recent basic and clinical data that point to a more balanced view of the detrimental and beneficial consequences of coagulation activation in sepsis. Reappraisal of the association between coagulation and immune activation from an evolutionary medicine perspective offers a unique opportunity to gain new insights about the pathogenesis of sepsis, paving the way to more successful approaches in both basic and clinical research in this field.

Mining protein database using machine learning techniques.

PubMed

Camargo, Renata da Silva; Niranjan, Mahesan

2008-08-25

With a large amount of information relating to proteins accumulating in databases widely available online, it is of interest to apply machine learning techniques that, by extracting underlying statistical regularities in the data, make predictions about the functional and evolutionary characteristics of unseen proteins. Such predictions can help in achieving a reduction in the space over which experiment designers need to search in order to improve our understanding of the biochemical properties. Previously it has been suggested that an integration of features computable by comparing a pair of proteins can be achieved by an artificial neural network, hence predicting the degree to which they may be evolutionary related and homologous.
We compiled two datasets of pairs of proteins, each pair being characterised by seven distinct features. We performed an exhaustive search through all possible combinations of features, for the problem of separating remote homologous from analogous pairs, we note that significant performance gain was obtained by the inclusion of sequence and structure information. We find that the use of a linear classifier was enough to discriminate a protein pair at the family level. However, at the superfamily level, to detect remote homologous pairs was a relatively harder problem. We find that the use of nonlinear classifiers achieve significantly higher accuracies.
In this paper, we compare three different pattern classification methods on two problems formulated as detecting evolutionary and functional relationships between pairs of proteins, and from extensive cross validation and feature selection based studies quantify the average limits and uncertainties with which such predictions may be made. Feature selection points to a \\"knowledge gap\\" in currently available functional annotations. We demonstrate how the scheme may be employed in a framework to associate an individual protein with an existing family of evolutionarily related proteins.

Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data

PubMed Central

Moore, Carrie B.; Wallace, John R.; Wolfe, Daniel J.; Frase, Alex T.; Pendergrass, Sarah A.; Weiss, Kenneth M.; Ritchie, Marylyn D.

2013-01-01

Analyses investigating low frequency variants have the potential for explaining additional genetic heritability of many complex human traits. However, the natural frequencies of rare variation between human populations strongly confound genetic analyses. We have applied a novel collapsing method to identify biological features with low frequency variant burden differences in thirteen populations sequenced by the 1000 Genomes Project. Our flexible collapsing tool utilizes expert biological knowledge from multiple publicly available database sources to direct feature selection. Variants were collapsed according to genetically driven features, such as evolutionary conserved regions, regulatory regions genes, and pathways. We have conducted an extensive comparison of low frequency variant burden differences (MAF<0.03) between populations from 1000 Genomes Project Phase I data. We found that on average 26.87% of gene bins, 35.47% of intergenic bins, 42.85% of pathway bins, 14.86% of ORegAnno regulatory bins, and 5.97% of evolutionary conserved regions show statistically significant differences in low frequency variant burden across populations from the 1000 Genomes Project. The proportion of bins with significant differences in low frequency burden depends on the ancestral similarity of the two populations compared and types of features tested. Even closely related populations had notable differences in low frequency burden, but fewer differences than populations from different continents. Furthermore, conserved or functionally relevant regions had fewer significant differences in low frequency burden than regions under less evolutionary constraint. This degree of low frequency variant differentiation across diverse populations and feature elements highlights the critical importance of considering population stratification in the new era of DNA sequencing and low frequency variant genomic analyses. PMID:24385916

Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

PubMed

Shackelford, Todd K; Liddle, James R

2014-05-01

The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

Evolutionary history of callose synthases in terrestrial plants with emphasis on proteins involved in male gametophyte development

PubMed Central

Honys, David

2017-01-01

Callose is a plant-specific polysaccharide (β-1,3-glucan) playing an important role in angiosperms in many developmental processes and responses to biotic and abiotic stresses. Callose is synthesised at the plasma membrane of plant cells by callose synthase (CalS) and, among others, represents the main polysaccharide in the callose wall surrounding the tetrads of developing microspores and in the growing pollen tube wall. CalS proteins involvement in spore development is a plesiomorphic feature of terrestrial plants, but very little is known about their evolutionary origin and relationships amongst the members of this protein family. We performed thorough comparative analyses of callose synthase family proteins from major plant lineages to determine their evolutionary history across the plant kingdom. A total of 1211 candidate CalS sequences were identified and compared amongst diverse taxonomic groups of plants, from bryophytes to angiosperms. Phylogenetic analyses identified six main clades of CalS proteins and suggested duplications during the evolution of specialised functions. Twelve family members had previously been identified in Arabidopsis thaliana. We focused on five CalS subfamilies directly linked to pollen function and found that proteins expressed in pollen evolved twice. CalS9/10 and CalS11/12 formed well-defined clades, whereas pollen-specific CalS5 was found within subfamilies that mostly did not express in mature pollen vegetative cell, although were found in sperm cells. Expression of five out of seven mature pollen-expressed CalS genes was affected by mutations in bzip transcription factors. Only three subfamilies, CalS5, CalS10, and CalS11, however, formed monophyletic, mostly conserved clades. The pairs CalS9/CalS10, CalS11/CalS12 and CalS3 may have diverged after angiosperms diversified from lycophytes and bryophytes. Our analysis of fully sequenced plant proteins identified new evolutionary lineages of callose synthase subfamilies and has established a basis for understanding their functional evolution in terrestrial plants. PMID:29131847

Different perspectives on the sex-attachment link: towards an emotion-motivational account.

PubMed

Dewitte, Marieke

2012-01-01

Although the link between sex and attachment was made decades ago (Hazan & Shaver, 1987), theories on sexual and attachment functioning have been developed in relative isolation. Recent efforts to integrate both literatures have been complicated by the fact that the sex-attachment link has been approached from very different perspectives, including biological, evolutionary, developmental, cognitive, and social psychology approaches. Also, at the empirical level, research on sex and attachment lacks overarching synthesis. This article gives an overview of the most important theoretical ideas and empirical insights on sex and attachment. It starts with describing general models that approach the sex-attachment link from an evolutionary and neurobiological perspective. Then, it summarizes theoretical and empirical ideas of attachment theory and describes how attachment style differences are manifested in intimate and sexual relationships. Research so far has been limited to studying the predicted link between sex and attachment in terms of broad descriptives, and it would benefit the literature to specify the processes and pathways that mediate the sex-attachment link. After a short discussion of the functional similarities between the sexual and the attachment systems, the article describes some specific--dynamical--models that focus on the emotional and cognitive-motivational processes through which attachment schemas influence sexual experiences. Such an emotion-motivational perspective on sex and attachment can help to organize theoretical ideas and empirical findings and eventually promote an integrative view on how attachment dynamics can interact with sexual experiences.

New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: implications for the host-fungal interactions

PubMed Central

2014-01-01

Background Aquaporins (AQPs) and aquaglyceroporins (AQGPs) belong to the superfamily of Major Intrinsic Proteins (MIPs) and are involved in the transport of water and neutral solutes across the membranes. MIP channels play significant role in plant-fungi symbiotic relationship and are believed to be important in host-pathogen interactions in human fungal diseases. In plants, at least five major MIP subfamilies have been identified. Fungal MIP subfamilies include orthodox aquaporins and five subgroups within aquaglyceroporins. XIP subfamily is common to both plants and fungi. In this study, we have investigated the extent of diversity in fungal MIPs and explored further evolutionary relationships with the plant MIP counterparts. Results We have extensively analyzed the available fungal genomes and examined nearly 400 fungal MIPs. Phylogenetic analysis and homology modeling exhibit the existence of a new MIP cluster distinct from any of the known fungal MIP subfamilies. All members of this cluster are found in microsporidia which are unicellular fungal parasites. Members of this family are small in size, charged and have hydrophobic residues in the aromatic/arginine selectivity filter and these features are shared by small and basic intrinsic proteins (SIPs), one of the plant MIP subfamilies. We have also found two new subfamilies (δ and γ2) within the AQGP group. Fungal AQGPs are the most diverse and possess the largest number of subgroups. We have also identified distinguishing features in loops E and D in the newly identified subfamilies indicating their possible role in channel transport and gating. Conclusions Fungal SIP-like MIP family is distinct from any of the known fungal MIP families including orthodox aquaporins and aquaglyceroporins. After XIPs, this is the second MIP subfamily from fungi that may have possible evolutionary link with a plant MIP subfamily. AQGPs in fungi are more diverse and possess the largest number of subgroups. The aromatic/arginine selectivity filter of SIP-like fungal MIPs and the δ AQGPs are unique, hydrophobic in nature and are likely to transport novel hydrophobic solutes. They can be attractive targets for developing anti-fungal drugs. The evolutionary pattern shared with their plant counterparts indicates possible involvement of new fungal MIPs in plant-fungi symbiosis and host-pathogen interactions. PMID:25112373

Glimpsing over the event horizon: evolution of nuclear pores and envelope.

PubMed

Jékely, Gáspár

2005-02-01

The origin of eukaryotes from prokaryotic ancestors is one of the major evolutionary transitions in the history of life. The nucleus, a membrane bound compartment for confining the genome, is a central feature of eukaryotic cells and its origin also has to be a central feature of any workable theory that ventures to explain eukaryotic origins. Recent bioinformatic analyses of components of the nuclear pore complex (NPC), the nuclear envelope (NE), and the nuclear transport systems revealed exciting evolutionary connections (e.g., between NPC and coated vesicles) and provided a useful record of the phyletic distribution and history of NPC and NE components. These analyses allow us to refine theories on the origin and evolution of the nucleus, and consequently, of the eukaryotic cell.

Female cats, but not males, adjust responsiveness to arousal in the voice of kittens.

PubMed

Konerding, Wiebke S; Zimmermann, Elke; Bleich, Eva; Hedrich, Hans-Jürgen; Scheumann, Marina

2016-08-12

The infant cry is the most important communicative tool to elicit adaptive parental behaviour. Sex-specific adaptation, linked to parental investment, may have evolutionary shaped the responsiveness to changes in the voice of the infant cries. The emotional content of infant cries may trigger distinctive responsiveness either based on their general arousing properties, being part of a general affect encoding rule, or based on affective perception, linked to parental investment, differing between species. To address this question, we performed playback experiments using infant isolation calls in a species without paternal care, the domestic cat. We used kitten calls recorded in isolation contexts inducing either Low arousal (i.e., isolation only) or High arousal (i.e., additional handling), leading to respective differences in escape response of the kittens. We predicted that only females respond differently to playbacks of Low versus High arousal kitten isolation calls, based on sex-differences in parental investment. Findings showed sex-specific responsiveness of adult cats listening to kitten isolation calls of different arousal conditions, with only females responding faster towards calls of the High versus the Low arousal condition. Breeding experience of females did not affect the result. Furthermore, female responsiveness correlated with acoustic parameters related to spectral characteristics of the fundamental frequency (F0): Females responded faster to kitten calls with lower F0 at call onset, lower minimum F0 and a steeper slope of the F0. Our study revealed sex-specific differences in the responsiveness to kitten isolation calls of different arousal conditions independent of female breeding experience. The findings indicated that features of F0 are important to convey the arousal state of an infant. Taken together, the results suggest that differences in parental investment evolutionary shaped responsiveness (auditory sensitivity/ motivation) to infant calls in a sex-specific manner in the domestic cat.

Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species.

PubMed

Walker, Michael B; King, Benjamin L; Paigen, Kenneth

2012-01-01

Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity.Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml) describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters) in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.

Crassulacean acid metabolism and epiphytism linked to adaptive radiations in the Orchidaceae.

PubMed

Silvera, Katia; Santiago, Louis S; Cushman, John C; Winter, Klaus

2009-04-01

Species of the large family Orchidaceae display a spectacular array of adaptations and rapid speciations that are linked to several innovative features, including specialized pollination syndromes, colonization of epiphytic habitats, and the presence of Crassulacean acid metabolism (CAM), a water-conserving photosynthetic pathway. To better understand the role of CAM and epiphytism in the evolutionary expansion of tropical orchids, we sampled leaf carbon isotopic composition of 1,103 species native to Panama and Costa Rica, performed character state reconstruction and phylogenetic trait analysis of CAM and epiphytism, and related strong CAM, present in 10% of species surveyed, to climatic variables and the evolution of epiphytism in tropical regions. Altitude was the most important predictor of photosynthetic pathway when all environmental variables were taken into account, with CAM being most prevalent at low altitudes. By creating integrated orchid trees to reconstruct ancestral character states, we found that C3 photosynthesis is the ancestral state and that CAM has evolved at least 10 independent times with several reversals. A large CAM radiation event within the Epidendroideae, the most species-rich epiphytic clade of any known plant group, is linked to a Tertiary species radiation that originated 65 million years ago. Our study shows that parallel evolution of CAM is present among subfamilies of orchids, and correlated divergence between photosynthetic pathways and epiphytism can be explained by the prevalence of CAM in low-elevation epiphytes and rapid speciation of high-elevation epiphytes in the Neotropics, contributing to the astounding diversity in the Orchidaceae.

Evolutionary considerations on complex emotions and music-induced emotions. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Gingras, Bruno; Marin, Manuela M.

2015-06-01

Recent efforts to uncover the neural underpinnings of emotional experiences have provided a foundation for novel neurophysiological theories of emotions, adding to the existing body of psychophysiological, motivational, and evolutionary theories. Besides explicitly modeling human-specific emotions and considering the interactions between emotions and language, Koelsch et al.'s original contribution to this challenging endeavor is to identify four brain areas as distinct "affect systems" which differ in terms of emotional qualia and evolutionary pathways [1]. Here, we comment on some features of this promising Quartet Theory of Emotions, focusing particularly on evolutionary and biological aspects related to the four affect systems and their relation to prevailing emotion theories, as well as on the role of music-induced emotions.

Feature theory and the two-step hypothesis of Müllerian mimicry evolution.

PubMed

Balogh, Alexandra Catherine Victoria; Gamberale-Stille, Gabriella; Tullberg, Birgitta Sillén; Leimar, Olof

2010-03-01

The two-step hypothesis of Müllerian mimicry evolution states that mimicry starts with a major mutational leap between adaptive peaks, followed by gradual fine-tuning. The hypothesis was suggested to solve the problem of apostatic selection producing a valley between adaptive peaks, and appears reasonable for a one-dimensional phenotype. Extending the hypothesis to the realistic scenario of multidimensional phenotypes controlled by multiple genetic loci can be problematic, because it is unlikely that major mutational leaps occur simultaneously in several traits. Here we consider the implications of predator psychology on the evolutionary process. According to feature theory, single prey traits may be used by predators as features to classify prey into discrete categories. A mutational leap in such a trait could initiate mimicry evolution. We conducted individual-based evolutionary simulations in which virtual predators both categorize prey according to features and generalize over total appearances. We found that an initial mutational leap toward feature similarity in one dimension facilitates mimicry evolution of multidimensional traits. We suggest that feature-based predator categorization together with predator generalization over total appearances solves the problem of applying the two-step hypothesis to complex phenotypes, and provides a basis for a theory of the evolution of mimicry rings.

Losing history: how extinctions prune features from the tree of life.

PubMed

Davies, T Jonathan

2015-02-19

Biodiversity provides many valuable services to humanity; however, rapid expansion of the human population has placed increasing pressure on natural systems, and it has been suggested that we may be entering a sixth mass extinction. There is an urgent need, therefore, to prioritize conservation efforts if we are to maintain the provisioning of such service in the future. Phylogenetic diversity (PD), the summed branch lengths that connect species on the tree-of-life, might provide a valuable metric for conservation prioritization because it has been argued to capture feature diversity. Frequently, PD is estimated in millions of years, and therefore implicitly assumes an evolutionary model in which features diverge gradually over time. Here, I explore the expected loss of feature diversity when this assumption is violated. If evolution tends to slow down over time, as might be the case following adaptive radiations, losses of feature diversity might be relatively small. However, if evolution occurs in rapid bursts, following a punctuated model, impacts of extinctions might be much greater. PD captures many important properties, but if we use it as a proxy for feature diversity, we first need to ensure that we have the correct evolutionary model. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Chromosomal Context Affects the Molecular Evolution of Sex-linked Genes and Their Autosomal Counterparts in Turtles and Other Vertebrates.

PubMed

Radhakrishnan, Srihari; Valenzuela, Nicole

2017-10-30

Sex chromosomes evolve differently from autosomes because natural selection acts distinctly on them given their reduced recombination and smaller population size. Various studies of sex-linked genes compared with different autosomal genes within species support these predictions. Here, we take a novel alternative approach by comparing the rate of evolution between subsets of genes that are sex-linked in selected reptiles/vertebrates and the same genes located in autosomes in other amniotes. We report for the first time the faster evolution of Z-linked genes in a turtle (the Chinese softshell turtle Pelodiscus sinensis) relative to autosomal orthologs in other taxa, including turtles with temperature-dependent sex determination (TSD). This faster rate was absent in its close relative, the spiny softshell turtle (Apalone spinifera), thus revealing important lineage effects, and was only surpassed by mammalian-X linked genes. In contrast, we found slower evolution of X-linked genes in the musk turtle Staurotypus triporcatus (XX/XY) and homologous Z-linked chicken genes. TSD lineages displayed overall faster sequence evolution than taxa with genotypic sex determination (GSD), ruling out global effects of GSD on molecular evolution beyond those by sex-linkage. Notably, results revealed a putative selective sweep around two turtle genes involved in vertebrate gonadogenesis (Pelodiscus-Z-linked Nf2 and Chrysemys-autosomal Tspan7). Our observations reveal important evolutionary changes at the gene level mediated by chromosomal context in turtles despite their low overall evolutionary rate and illuminate sex chromosome evolution by empirically testing expectations from theoretical models. Genome-wide analyses are warranted to test the generality and prevalence of the observed patterns. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

PubMed

Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

2014-11-11

Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

Preserving the evolutionary potential of floras in biodiversity hotspots.

PubMed

Forest, Félix; Grenyer, Richard; Rouget, Mathieu; Davies, T Jonathan; Cowling, Richard M; Faith, Daniel P; Balmford, Andrew; Manning, John C; Procheş, Serban; van der Bank, Michelle; Reeves, Gail; Hedderson, Terry A J; Savolainen, Vincent

2007-02-15

One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot--the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.

The adaptation of polar fishes to climatic changes: Structure, function and phylogeny of haemoglobin.

PubMed

Verde, Cinzia; Giordano, Daniela; di Prisco, Guido

2008-01-01

In the Antarctic, fishes of dominant suborder Notothenioidei have evolved in a unique thermal scenario. Phylogenetically related taxa of the suborder live in a wide range of latitudes, in Antarctic, sub-Antarctic and temperate oceans. Consequently, they offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history. The evolutionary perspective has also been pursued by comparative studies of some features of the heme protein devoted to O(2) transport in fish living in the other polar region, the Arctic. The two polar regions differ by age and isolation. Fish living in each habitat have undergone regional constraints and fit into different evolutionary histories. The aim of this contribution is to survey the current knowledge of molecular structure, functional features, phylogeny and adaptations of the haemoglobins of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes), in search of insights into the convergent processes evolved in response to cooling. Current climate change may disturb adaptation, calling for strategies aimed at neutralising threats to biodiversity.

Iris double recognition based on modified evolutionary neural network

NASA Astrophysics Data System (ADS)

Liu, Shuai; Liu, Yuan-Ning; Zhu, Xiao-Dong; Huo, Guang; Liu, Wen-Tao; Feng, Jia-Kai

2017-11-01

Aiming at multicategory iris recognition under illumination and noise interference, this paper proposes a method of iris double recognition based on a modified evolutionary neural network. An equalization histogram and Laplace of Gaussian operator are used to process the iris to suppress illumination and noise interference and Haar wavelet to convert the iris feature to binary feature encoding. Calculate the Hamming distance for the test iris and template iris , and compare with classification threshold, determine the type of iris. If the iris cannot be identified as a different type, there needs to be a secondary recognition. The connection weights in back-propagation (BP) neural network use modified evolutionary neural network to adaptively train. The modified neural network is composed of particle swarm optimization with mutation operator and BP neural network. According to different iris libraries in different circumstances of experimental results, under illumination and noise interference, the correct recognition rate of this algorithm is higher, the ROC curve is closer to the coordinate axis, the training and recognition time is shorter, and the stability and the robustness are better.

Hidden genetic variation in the germline genome of Tetrahymena thermophila.

PubMed

Dimond, K L; Zufall, R A

2016-06-01

Genome architecture varies greatly among eukaryotes. This diversity may profoundly affect the origin and maintenance of genetic variation within a population. Ciliates are microbial eukaryotes with unusual genome features, such as the separation of germline and somatic genomes within a single cell and amitotic division. These features have previously been proposed to increase the rate of molecular evolution in these species. Here, we assessed the fitness effects of genetic variation in the two genomes of natural isolates of the ciliate Tetrahymena thermophila. We find more extensive genetic variation in fitness in the transcriptionally silent germline genome than in the expressed somatic genome. Surprisingly, this variation is not primarily deleterious, but has both beneficial and deleterious effects. We conclude that Tetrahymena genome architecture allows for the maintenance of genetic variation that would otherwise be eliminated by selection. We consider the effect of selection on the two genomes and the impacts of reproductive strategies and the mechanism of sex determination on the structure of this variation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

New understanding of adolescent brain development: relevance to transitional healthcare for young people with long term conditions.

PubMed

Colver, Allan; Longwell, Sarah

2013-11-01

Whether or not adolescence should be treated as a special period, there is now no doubt that the brain changes much during adolescence. From an evolutionary perspective, the idea of an under developed brain which is not fit for purpose until adulthood is illogical. Rather, the adolescent brain is likely to support the challenges specific to that period of life. New imaging techniques show striking changes in white and grey matter between 11 and 25 years of age, with increased connectivity between brain regions, and increased dopaminergic activity in the pre-frontal cortices, striatum and limbic system and the pathways linking them. The brain is dynamic, with some areas developing faster and becoming more dominant until other areas catch up. Plausible mechanisms link these changes to cognitive and behavioural features of adolescence. The changing brain may lead to abrupt behavioural change with attendant risks, but such a brain is flexible and can respond quickly and imaginatively. Society allows adolescent exuberance and creativity to be bounded and explored in relative safety. In healthcare settings these changes are especially relevant to young people with long term conditions as they move to young adult life; such young people need to learn to manage their health conditions with the support of their healthcare providers.

Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

PubMed

Huang, Bing-Hong; Liao, Pei-Chun

2015-07-01

Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Learning Spatio-Temporal Representations for Action Recognition: A Genetic Programming Approach.

PubMed

Liu, Li; Shao, Ling; Li, Xuelong; Lu, Ke

2016-01-01

Extracting discriminative and robust features from video sequences is the first and most critical step in human action recognition. In this paper, instead of using handcrafted features, we automatically learn spatio-temporal motion features for action recognition. This is achieved via an evolutionary method, i.e., genetic programming (GP), which evolves the motion feature descriptor on a population of primitive 3D operators (e.g., 3D-Gabor and wavelet). In this way, the scale and shift invariant features can be effectively extracted from both color and optical flow sequences. We intend to learn data adaptive descriptors for different datasets with multiple layers, which makes fully use of the knowledge to mimic the physical structure of the human visual cortex for action recognition and simultaneously reduce the GP searching space to effectively accelerate the convergence of optimal solutions. In our evolutionary architecture, the average cross-validation classification error, which is calculated by an support-vector-machine classifier on the training set, is adopted as the evaluation criterion for the GP fitness function. After the entire evolution procedure finishes, the best-so-far solution selected by GP is regarded as the (near-)optimal action descriptor obtained. The GP-evolving feature extraction method is evaluated on four popular action datasets, namely KTH, HMDB51, UCF YouTube, and Hollywood2. Experimental results show that our method significantly outperforms other types of features, either hand-designed or machine-learned.

Missing link in the evolution of Hox clusters.

PubMed

Ogishima, Soichi; Tanaka, Hiroshi

2007-01-31

Hox cluster has key roles in regulating the patterning of the antero-posterior axis in a metazoan embryo. It consists of the anterior, central and posterior genes; the central genes have been identified only in bilaterians, but not in cnidarians, and are responsible for archiving morphological complexity in bilaterian development. However, their evolutionary history has not been revealed, that is, there has been a "missing link". Here we show the evolutionary history of Hox clusters of 18 bilaterians and 2 cnidarians by using a new method, "motif-based reconstruction", examining the gain/loss processes of evolutionarily conserved sequences, "motifs", outside the homeodomain. We successfully identified the missing link in the evolution of Hox clusters between the cnidarian-bilaterian ancestor and the bilaterians as the ancestor of the central genes, which we call the proto-central gene. Exploring the correspondent gene with the proto-central gene, we found that one of the acoela Hox genes has the same motif repertory as that of the proto-central gene. This interesting finding suggests that the acoela Hox cluster corresponds with the missing link in the evolution of the Hox cluster between the cnidarian-bilaterian ancestor and the bilaterians. Our findings suggested that motif gains/diversifications led to the explosive diversity of the bilaterian body plan.

The exaptive excellence of spandrels as a term and prototype

PubMed Central

Gould, Stephen Jay

1997-01-01

In 1979, Lewontin and I borrowed the architectural term “spandrel” (using the pendentives of San Marco in Venice as an example) to designate the class of forms and spaces that arise as necessary byproducts of another decision in design, and not as adaptations for direct utility in themselves. This proposal has generated a large literature featuring two critiques: (i) the terminological claim that the spandrels of San Marco are not true spandrels at all and (ii) the conceptual claim that they are adaptations and not byproducts. The features of the San Marco pendentives that we explicitly defined as spandrel-properties—their necessary number (four) and shape (roughly triangular)—are inevitable architectural byproducts, whatever the structural attributes of the pendentives themselves. The term spandrel may be extended from its particular architectural use for two-dimensional byproducts to the generality of “spaces left over,” a definition that properly includes the San Marco pendentives. Evolutionary biology needs such an explicit term for features arising as byproducts, rather than adaptations, whatever their subsequent exaptive utility. The concept of biological spandrels—including the examples here given of masculinized genitalia in female hyenas, exaptive use of an umbilicus as a brooding chamber by snails, the shoulder hump of the giant Irish deer, and several key features of human mentality—anchors the critique of overreliance upon adaptive scenarios in evolutionary explanation. Causes of historical origin must always be separated from current utilities; their conflation has seriously hampered the evolutionary analysis of form in the history of life. PMID:11038582

CDMetaPOP: An individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics

USGS Publications Warehouse

Landguth, Erin L; Bearlin, Andrew; Day, Casey; Dunham, Jason B.

2016-01-01

1. Combining landscape demographic and genetics models offers powerful methods for addressing questions for eco-evolutionary applications.2. Using two illustrative examples, we present Cost–Distance Meta-POPulation, a program to simulate changes in neutral and/or selection-driven genotypes through time as a function of individual-based movement, complex spatial population dynamics, and multiple and changing landscape drivers.3. Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

Dynamic and scalable audio classification by collective network of binary classifiers framework: an evolutionary approach.

PubMed

Kiranyaz, Serkan; Mäkinen, Toni; Gabbouj, Moncef

2012-10-01

In this paper, we propose a novel framework based on a collective network of evolutionary binary classifiers (CNBC) to address the problems of feature and class scalability. The main goal of the proposed framework is to achieve a high classification performance over dynamic audio and video repositories. The proposed framework adopts a "Divide and Conquer" approach in which an individual network of binary classifiers (NBC) is allocated to discriminate each audio class. An evolutionary search is applied to find the best binary classifier in each NBC with respect to a given criterion. Through the incremental evolution sessions, the CNBC framework can dynamically adapt to each new incoming class or feature set without resorting to a full-scale re-training or re-configuration. Therefore, the CNBC framework is particularly designed for dynamically varying databases where no conventional static classifiers can adapt to such changes. In short, it is entirely a novel topology, an unprecedented approach for dynamic, content/data adaptive and scalable audio classification. A large set of audio features can be effectively used in the framework, where the CNBCs make appropriate selections and combinations so as to achieve the highest discrimination among individual audio classes. Experiments demonstrate a high classification accuracy (above 90%) and efficiency of the proposed framework over large and dynamic audio databases. Copyright © 2012 Elsevier Ltd. All rights reserved.

OH masers towards IRAS 19092+0841

NASA Astrophysics Data System (ADS)

Edris, K. A.; Fuller, G. A.; Etoka, S.; Cohen, R. J.

2017-12-01

Context. Maser emission is a strong tool for studying high-mass star-forming regions and their evolutionary stages. OH masers in particular can trace the circumstellar material around protostars and determine their magnetic field strengths at milliarcsecond resolution. Aims: We seek to image OH maser emission towards high-mass protostellar objects to determine their evolutionary stages and to locate the detected maser emission in the process of high-mass star formation. Methods: In 2007, we surveyed OH maser emission towards 217 high-mass protostellar objects to study its presence. In this paper, we present follow-up MERLIN observations of a ground-state OH maser emission towards one of these objects, IRAS 19092+0841. Results: We detect emissions from the two OH main spectral lines, 1665 and 1667 MHz, close to the central object. We determine the positions and velocities of the OH maser features. The masers are distributed over a region of 5'' corresponding to 22 400 AU (or 0.1 pc) at a distance of 4.48 kpc. The polarization properties of the OH maser features are determined as well. We identify three Zeeman pairs from which we inferred a magnetic field strength of 4.4 mG pointing towards the observer. Conclusions: The relatively small velocity spread and relatively wide spacial distribution of the OH maser features support the suggestion that this object could be in an early evolutionary state before the presence of disk, jets or outflows.

Pancreatic cancer biology and genetics from an evolutionary perspective

PubMed Central

Makohon-Moore, Alvin; Iacobuzio-Donahue, Christine A.

2017-01-01

Cancer is an evolutionary disease, containing the hallmarks of an asexually reproducing unicellular organism subject to evolutionary paradigms. Pancreatic ductal adenocarcinoma (hereafter referred to as pancreatic cancer) is a particularly robust example of this phenomenon. Genomic features indicate that pancreatic cancer cells are selected for fitness advantages when encountering the geographic and resource-depleted constraints of the microenvironment. Phenotypic adaptations to these pressures help disseminated cells to survive in secondary sites, a major clinical problem for patients with this disease. In this Review we gather the wide-ranging aspects of pancreatic cancer research into a single concept rooted in Darwinian evolution, with the goal of identifying novel insights and opportunities for study. PMID:27444064

Packets Distributing Evolutionary Algorithm Based on PSO for Ad Hoc Network

NASA Astrophysics Data System (ADS)

Xu, Xiao-Feng

2018-03-01

Wireless communication network has such features as limited bandwidth, changeful channel and dynamic topology, etc. Ad hoc network has lots of difficulties in accessing control, bandwidth distribution, resource assign and congestion control. Therefore, a wireless packets distributing Evolutionary algorithm based on PSO (DPSO)for Ad Hoc Network is proposed. Firstly, parameters impact on performance of network are analyzed and researched to obtain network performance effective function. Secondly, the improved PSO Evolutionary Algorithm is used to solve the optimization problem from local to global in the process of network packets distributing. The simulation results show that the algorithm can ensure fairness and timeliness of network transmission, as well as improve ad hoc network resource integrated utilization efficiency.

Evolutionary grinding model for nanometric control of surface roughness for aspheric optical surfaces.

PubMed

Han, Jeong-Yeol; Kim, Sug-Whan; Han, Inwoo; Kim, Geon-Hee

2008-03-17

A new evolutionary grinding process model has been developed for nanometric control of material removal from an aspheric surface of Zerodur substrate. The model incorporates novel control features such as i) a growing database; ii) an evolving, multi-variable regression equation; and iii) an adaptive correction factor for target surface roughness (Ra) for the next machine run. This process model demonstrated a unique evolutionary controllability of machining performance resulting in the final grinding accuracy (i.e. averaged difference between target and measured surface roughness) of -0.2+/-2.3(sigma) nm Ra over seven trial machine runs for the target surface roughness ranging from 115 nm to 64 nm Ra.

Morphological variation in salamanders and their potential response to climate change.

PubMed

Ficetola, Gentile Francesco; Colleoni, Emiliano; Renaud, Julien; Scali, Stefano; Padoa-Schioppa, Emilio; Thuiller, Wilfried

2016-06-01

Despite the recognition that some species might quickly adapt to new conditions under climate change, demonstrating and predicting such a fundamental response is challenging. Morphological variations in response to climate may be caused by evolutionary changes or phenotypic plasticity, or both, but teasing apart these processes is difficult. Here, we built on the number of thoracic vertebrae (NTV) in ectothermic vertebrates, a known genetically based feature, to establish a link with body size and evaluate how climate change might affect the future morphological response of this group of species. First, we show that in old-world salamanders, NTV variation is strongly related to changes in body size. Secondly, using 22 salamander species as a case study, we found support for relationships between the spatial variation in selected bioclimatic variables and NTV for most of species. For 44% of species, precipitation and aridity were the predominant drivers of geographical variation of the NTV. Temperature features were dominant for 31% of species, while for 19% temperature and precipitation played a comparable role. This two-step analysis demonstrates that ectothermic vertebrates may evolve in response to climate change by modifying the number of thoracic vertebrae. These findings allow to develop scenarios for potential morphological evolution under future climate change and to identify areas and species in which the most marked evolutionary responses are expected. Resistance to climate change estimated from species distribution models was positively related to present-day species morphological response, suggesting that the ability of morphological evolution may play a role for species' persistence under climate change. The possibility that present-day capacity for local adaptation might help the resistance response to climate change can be integrated into analyses of the impact of global changes and should also be considered when planning management actions favouring species persistence. © 2016 John Wiley & Sons Ltd.

The Neural Systems of Forgiveness: An Evolutionary Psychological Perspective

PubMed Central

Billingsley, Joseph; Losin, Elizabeth A. R.

2017-01-01

Evolution-minded researchers posit that the suite of human cognitive adaptations may include forgiveness systems. According to these researchers, forgiveness systems regulate interpersonal motivation toward a transgressor in the wake of harm by weighing multiple factors that influence both the potential gains of future interaction with the transgressor and the likelihood of future harm. Although behavioral research generally supports this evolutionary model of forgiveness, the model’s claims have not been examined with available neuroscience specifically in mind, nor has recent neuroscientific research on forgiveness generally considered the evolutionary literature. The current review aims to help bridge this gap by using evolutionary psychology and cognitive neuroscience to mutually inform and interrogate one another. We briefly summarize the evolutionary research on forgiveness, then review recent neuroscientific findings on forgiveness in light of the evolutionary model. We emphasize neuroscientific research that links desire for vengeance to reward-based areas of the brain, that singles out prefrontal areas likely associated with inhibition of vengeful feelings, and that correlates the activity of a theory-of-mind network with assessments of the intentions and blameworthiness of those who commit harm. In addition, we identify gaps in the existing neuroscientific literature, and propose future research directions that might address them, at least in part. PMID:28539904

Evolutionary cell biology: two origins, one objective.

PubMed

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

2014-12-02

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

Evolutionary cell biology: Two origins, one objective

PubMed Central

Lynch, Michael; Field, Mark C.; Goodson, Holly V.; Malik, Harmit S.; Pereira-Leal, José B.; Roos, David S.; Turkewitz, Aaron P.; Sazer, Shelley

2014-01-01

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. PMID:25404324

Conservation Evo-Devo: Preserving Biodiversity by Understanding Its Origins.

PubMed

Campbell, Calum S; Adams, Colin E; Bean, Colin W; Parsons, Kevin J

2017-10-01

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

PubMed Central

Solé, Ricard V; Montoya, José M; Erwin, Douglas H

2002-01-01

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems. PMID:12079530

Within-population Y-linked genetic variation for lifespan in Drosophila melanogaster.

PubMed

Griffin, R M; Le Gall, D; Schielzeth, H; Friberg, U

2015-11-01

The view that the Y chromosome is of little importance for phenotypic evolution stems from early studies of Drosophila melanogaster. This species' Y chromosome contains only 13 protein-coding genes, is almost entirely heterochromatic and is not necessary for male viability. Population genetic theory further suggests that non-neutral variation can only be maintained at the Y chromosome under special circumstances. Yet, recent studies suggest that the D. melanogaster Y chromosome trans-regulates hundreds to thousands of X and autosomal genes. This finding suggests that the Y chromosome may play a far more active role in adaptive evolution than has previously been assumed. To evaluate the potential for the Y chromosome to contribute to phenotypic evolution from standing genetic variation, we test for Y-linked variation in lifespan within a population of D. melanogaster. Assessing variation for lifespan provides a powerful test because lifespan (i) shows sexual dimorphism, which the Y is primarily predicted to contribute to, (ii) is influenced by many genes, which provides the Y with many potential regulatory targets and (iii) is sensitive to heterochromatin remodelling, a mechanism through which the Y chromosome is believed to regulate gene expression. Our results show a small but significant effect of the Y chromosome and thus suggest that the Y chromosome has the potential to respond to selection from standing genetic variation. Despite its small effect size, Y-linked variation may still be important, in particular when evolution of sexual dimorphism is genetically constrained elsewhere in the genome. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

An evolutionary concept of polycystic ovarian disease: does evolution favour reproductive success over survival?

PubMed

Gleicher, Norbert; Barad, David

2006-05-01

Polycystic ovarian disease (PCOD) is currently considered as possibly the most frequent cause of female infertility. It is also closely associated with syndrome XX, which, in turn, is closely linked with premature and excessive mortality. Considering these adverse effects on reproductive success and human survival, the evolutionary survival of PCOD, itself considered by many to be a genetically transmitted condition, would, on first glance, appear surprising, since evolution usually discriminates against both of these traits. However, an analysis of some recently reported characteristics of the condition calls for the reconsideration of PCOD as a condition which, from an evolutionary viewpoint, favours decreased reproductive success. Indeed, the reported observations that patients with PCOD will resume spontaneous ovulation with even relatively minor weight loss, and experience later menopause than controls, suggests exactly the opposite. Under an evolutionary concept, PCOD can thus be seen as a 'fertility storage condition' which in fact favours human reproductive success and allows the human species to maintain fertility even during adverse environmental circumstances, such as famines.

Evolutionary games on graphs

NASA Astrophysics Data System (ADS)

Szabó, György; Fáth, Gábor

2007-07-01

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

A new evolutionary system for evolving artificial neural networks.

PubMed

Yao, X; Liu, Y

1997-01-01

This paper presents a new evolutionary system, i.e., EPNet, for evolving artificial neural networks (ANNs). The evolutionary algorithm used in EPNet is based on Fogel's evolutionary programming (EP). Unlike most previous studies on evolving ANN's, this paper puts its emphasis on evolving ANN's behaviors. Five mutation operators proposed in EPNet reflect such an emphasis on evolving behaviors. Close behavioral links between parents and their offspring are maintained by various mutations, such as partial training and node splitting. EPNet evolves ANN's architectures and connection weights (including biases) simultaneously in order to reduce the noise in fitness evaluation. The parsimony of evolved ANN's is encouraged by preferring node/connection deletion to addition. EPNet has been tested on a number of benchmark problems in machine learning and ANNs, such as the parity problem, the medical diagnosis problems, the Australian credit card assessment problem, and the Mackey-Glass time series prediction problem. The experimental results show that EPNet can produce very compact ANNs with good generalization ability in comparison with other algorithms.

The evolutionary ecology of complex lifecycle parasites: linking phenomena with mechanisms

PubMed Central

Auld, S KJR; Tinsley, M C

2015-01-01

Many parasitic infections, including those of humans, are caused by complex lifecycle parasites (CLPs): parasites that sequentially infect different hosts over the course of their lifecycle. CLPs come from a wide range of taxonomic groups—from single-celled bacteria to multicellular flatworms—yet share many common features in their life histories. Theory tells us when CLPs should be favoured by selection, but more empirical studies are required in order to quantify the costs and benefits of having a complex lifecycle, especially in parasites that facultatively vary their lifecycle complexity. In this article, we identify ecological conditions that favour CLPs over their simple lifecycle counterparts and highlight how a complex lifecycle can alter transmission rate and trade-offs between growth and reproduction. We show that CLPs participate in dynamic host–parasite coevolution, as more mobile hosts can fuel CLP adaptation to less mobile hosts. Then, we argue that a more general understanding of the evolutionary ecology of CLPs is essential for the development of effective frameworks to manage the many diseases they cause. More research is needed identifying the genetics of infection mechanisms used by CLPs, particularly into the role of gene duplication and neofunctionalisation in lifecycle evolution. We propose that testing for signatures of selection in infection genes will reveal much about how and when complex lifecycles evolved, and will help quantify complex patterns of coevolution between CLPs and their various hosts. Finally, we emphasise four key areas where new research approaches will provide fertile opportunities to advance this field. PMID:25227255

The Crystal Structure of Giardia duodenalis 14-3-3 in the Apo Form: When Protein Post-Translational Modifications Make the Difference

PubMed Central

Fiorillo, Annarita; di Marino, Daniele; Bertuccini, Lucia; Via, Allegra; Pozio, Edoardo; Camerini, Serena; Ilari, Andrea; Lalle, Marco

2014-01-01

The 14-3-3s are a family of dimeric evolutionary conserved pSer/pThr binding proteins that play a key role in multiple biological processes by interacting with a plethora of client proteins. Giardia duodenalis is a flagellated protozoan that affects millions of people worldwide causing an acute and chronic diarrheal disease. The single giardial 14-3-3 isoform (g14-3-3), unique in the 14-3-3 family, needs the constitutive phosphorylation of Thr214 and the polyglycylation of its C-terminus to be fully functional in vivo. Alteration of the phosphorylation and polyglycylation status affects the parasite differentiation into the cyst stage. To further investigate the role of these post-translational modifications, the crystal structure of the g14-3-3 was solved in the unmodified apo form. Oligomers of g14-3-3 were observed due to domain swapping events at the protein C-terminus. The formation of filaments was supported by TEM. Mutational analysis, in combination with native PAGE and chemical cross-linking, proved that polyglycylation prevents oligomerization. In silico phosphorylation and molecular dynamics simulations supported a structural role for the phosphorylation of Thr214 in promoting target binding. Our findings highlight unique structural features of g14-3-3 opening novel perspectives on the evolutionary history of this protein family and envisaging the possibility to develop anti-giardial drugs targeting g14-3-3. PMID:24658679

Plant endemism in the Sierras of Córdoba and San Luis (Argentina): understanding links between phylogeny and regional biogeographical patterns1

PubMed Central

Chiapella, Jorge O.; Demaio, Pablo H.

2015-01-01

Abstract We compiled a checklist with all known endemic plants occurring in the Sierras of Córdoba and San Luis, an isolated mountainous range located in central Argentina. In order to obtain a better understanding of the evolutionary history, relationships and age of the regional flora, we gathered basic information on the biogeographical and floristic affinities of the endemics, and documented the inclusion of each taxon in molecular phylogenies. We listed 89 taxa (including 69 species and 20 infraspecific taxa) belonging to 53 genera and 29 families. The endemics are not distributed evenly, being more abundant in the lower than in the middle and upper vegetation belts. Thirty-two genera (60.3%) have been included in phylogenetic analyses, but only ten (18.8%) included local endemic taxa. A total of 28 endemic taxa of the Sierras CSL have a clear relationship with a widespread species of the same genus, or with one found close to the area. Available phylogenies for some taxa show divergence times between 7.0 – 1.8 Ma; all endemic taxa are most probably neoendemics sensu Stebbins and Major. Our analysis was specifically aimed at a particular geographic area, but the approach of analyzing phylogenetic patterns together with floristic or biogeographical relationships of the endemic taxa of an area, delimited by clear geomorphological features, could reveal evolutionary trends shaping the area. PMID:25878555

Robust enzyme design: bioinformatic tools for improved protein stability.

PubMed

Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

2015-03-01

The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolutionary and differential psychology: conceptual conflicts and the path to integration

PubMed Central

Marsh, Tim; Boag, Simon

2013-01-01

Evolutionary psychology has seen the majority of its success exploring adaptive features of the mind believed to be ubiquitous across our species. This has given rise to the belief that the adaptationist approach has little to offer the field of differential psychology, which concerns itself exclusively with the ways in which individuals systematically differ. By framing the historical origins of both disciplines, and exploring the means through which they each address the unique challenges of psychological description and explanation, the present article identifies the conceptual and theoretical problems that have kept differential psychology isolated not only from evolutionary psychology, but from explanatory approaches in general. Paying special attention to these conceptual problems, the authors review how these difficulties are being overcome by contemporary evolutionary research, and offer instructive suggestions concerning how differential researchers (and others) can best build upon these innovations. PMID:24065949

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Evolutionary genomics and HIV restriction factors.

PubMed

Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

2015-03-01

To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

Emergence of scale-free characteristics in socio-ecological systems with bounded rationality

PubMed Central

Kasthurirathna, Dharshana; Piraveenan, Mahendra

2015-01-01

Socio–ecological systems are increasingly modelled by games played on complex networks. While the concept of Nash equilibrium assumes perfect rationality, in reality players display heterogeneous bounded rationality. Here we present a topological model of bounded rationality in socio-ecological systems, using the rationality parameter of the Quantal Response Equilibrium. We argue that system rationality could be measured by the average Kullback–-Leibler divergence between Nash and Quantal Response Equilibria, and that the convergence towards Nash equilibria on average corresponds to increased system rationality. Using this model, we show that when a randomly connected socio-ecological system is topologically optimised to converge towards Nash equilibria, scale-free and small world features emerge. Therefore, optimising system rationality is an evolutionary reason for the emergence of scale-free and small-world features in socio-ecological systems. Further, we show that in games where multiple equilibria are possible, the correlation between the scale-freeness of the system and the fraction of links with multiple equilibria goes through a rapid transition when the average system rationality increases. Our results explain the influence of the topological structure of socio–ecological systems in shaping their collective cognitive behaviour, and provide an explanation for the prevalence of scale-free and small-world characteristics in such systems. PMID:26065713

Late Middle Pleistocene hominin teeth from Panxian Dadong, South China.

PubMed

Liu, Wu; Schepartz, Lynne A; Xing, Song; Miller-Antonio, Sari; Wu, Xiujie; Trinkaus, Erik; Martinón-Torres, María

2013-05-01

The hominin teeth and evidence of hominin activities recovered from 1991 to 2005 at the Panxian Dadong site in South China are dated to the late Middle Pleistocene (MIS 8-6 or ca. 130-300 ka), a period for which very little is known about the morphology of Asian populations. The present study provides the first detailed morphometric description and comparisons of four hominin teeth (I(1), C1, P(3) and P3) from this site. Our study shows that the Panxian Dadong teeth combine archaic and derived features that align them with Middle and Upper Pleistocene fossils from East and West Asia and Europe. These teeth do not display any typical Neanderthal features and they are generally more derived than other contemporaneous populations from Asia and Africa. However, the derived traits are not diagnostic enough to specifically link the Panxian Dadong teeth to Homo sapiens, a common problem when analyzing the Middle Pleistocene dental record from Africa and Asia. These findings are contextualized in the discussion of the evolutionary course of Asian Middle Pleistocene hominins, and they highlight the necessity of incorporating the Asian fossil record in the still open debate about the origin of H. sapiens. Copyright © 2013 Elsevier Ltd. All rights reserved.

Chloride Channelopathies of ClC-2

PubMed Central

Bi, Miao Miao; Hong, Sen; Zhou, Hong Yan; Wang, Hong Wei; Wang, Li Na; Zheng, Ya Juan

2014-01-01

Chloride channels (ClCs) have gained worldwide interest because of their molecular diversity, widespread distribution in mammalian tissues and organs, and their link to various human diseases. Nine different ClCs have been molecularly identified and functionally characterized in mammals. ClC-2 is one of nine mammalian members of the ClC family. It possesses unique biophysical characteristics, pharmacological properties, and molecular features that distinguish it from other ClC family members. ClC-2 has wide organ/tissue distribution and is ubiquitously expressed. Published studies consistently point to a high degree of conservation of ClC-2 function and regulation across various species from nematodes to humans over vast evolutionary time spans. ClC-2 has been intensively and extensively studied over the past two decades, leading to the accumulation of a plethora of information to advance our understanding of its pathophysiological functions; however, many controversies still exist. It is necessary to analyze the research findings, and integrate different views to have a better understanding of ClC-2. This review focuses on ClC-2 only, providing an analytical overview of the available literature. Nearly every aspect of ClC-2 is discussed in the review: molecular features, biophysical characteristics, pharmacological properties, cellular function, regulation of expression and function, and channelopathies. PMID:24378849

Emergence of scale-free characteristics in socio-ecological systems with bounded rationality.

PubMed

Kasthurirathna, Dharshana; Piraveenan, Mahendra

2015-06-11

Socio-ecological systems are increasingly modelled by games played on complex networks. While the concept of Nash equilibrium assumes perfect rationality, in reality players display heterogeneous bounded rationality. Here we present a topological model of bounded rationality in socio-ecological systems, using the rationality parameter of the Quantal Response Equilibrium. We argue that system rationality could be measured by the average Kullback--Leibler divergence between Nash and Quantal Response Equilibria, and that the convergence towards Nash equilibria on average corresponds to increased system rationality. Using this model, we show that when a randomly connected socio-ecological system is topologically optimised to converge towards Nash equilibria, scale-free and small world features emerge. Therefore, optimising system rationality is an evolutionary reason for the emergence of scale-free and small-world features in socio-ecological systems. Further, we show that in games where multiple equilibria are possible, the correlation between the scale-freeness of the system and the fraction of links with multiple equilibria goes through a rapid transition when the average system rationality increases. Our results explain the influence of the topological structure of socio-ecological systems in shaping their collective cognitive behaviour, and provide an explanation for the prevalence of scale-free and small-world characteristics in such systems.

Improving link prediction in complex networks by adaptively exploiting multiple structural features of networks

NASA Astrophysics Data System (ADS)

Ma, Chuang; Bao, Zhong-Kui; Zhang, Hai-Feng

2017-10-01

So far, many network-structure-based link prediction methods have been proposed. However, these methods only highlight one or two structural features of networks, and then use the methods to predict missing links in different networks. The performances of these existing methods are not always satisfied in all cases since each network has its unique underlying structural features. In this paper, by analyzing different real networks, we find that the structural features of different networks are remarkably different. In particular, even in the same network, their inner structural features are utterly different. Therefore, more structural features should be considered. However, owing to the remarkably different structural features, the contributions of different features are hard to be given in advance. Inspired by these facts, an adaptive fusion model regarding link prediction is proposed to incorporate multiple structural features. In the model, a logistic function combing multiple structural features is defined, then the weight of each feature in the logistic function is adaptively determined by exploiting the known structure information. Last, we use the "learnt" logistic function to predict the connection probabilities of missing links. According to our experimental results, we find that the performance of our adaptive fusion model is better than many similarity indices.

Multiobjective Multifactorial Optimization in Evolutionary Multitasking.

PubMed

Gupta, Abhishek; Ong, Yew-Soon; Feng, Liang; Tan, Kay Chen

2016-05-03

In recent decades, the field of multiobjective optimization has attracted considerable interest among evolutionary computation researchers. One of the main features that makes evolutionary methods particularly appealing for multiobjective problems is the implicit parallelism offered by a population, which enables simultaneous convergence toward the entire Pareto front. While a plethora of related algorithms have been proposed till date, a common attribute among them is that they focus on efficiently solving only a single optimization problem at a time. Despite the known power of implicit parallelism, seldom has an attempt been made to multitask, i.e., to solve multiple optimization problems simultaneously. It is contended that the notion of evolutionary multitasking leads to the possibility of automated transfer of information across different optimization exercises that may share underlying similarities, thereby facilitating improved convergence characteristics. In particular, the potential for automated transfer is deemed invaluable from the standpoint of engineering design exercises where manual knowledge adaptation and reuse are routine. Accordingly, in this paper, we present a realization of the evolutionary multitasking paradigm within the domain of multiobjective optimization. The efficacy of the associated evolutionary algorithm is demonstrated on some benchmark test functions as well as on a real-world manufacturing process design problem from the composites industry.

The Generation of Variation and The Developmental Basis for Evolutionary Novelty

PubMed Central

Hallgrímsson, Benedikt; Jamniczky, Heather A.; Young, Nathan M.; Rolian, Campbell; Schmidt-Ott, Urs; Marcucio, Ralph S.

2013-01-01

Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the “obvious” case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We instead propose that for a feature to be novel it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low probability evolutionary transitions and highlights how the integration of developmental and functional considerations is necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., “evo-devo”) but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle. PMID:22649039

Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels

PubMed Central

Lomash, Suvendu; Chittori, Sagar; Brown, Patrick; Mayer, Mark L.

2014-01-01

SUMMARY AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine and phenylalanine which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate and serine. AvGluR1 LBD crystal structures reveal a novel scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, while in the alanine, methionine and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl− lowers affinity for these ligands, but not for glutamate, aspartate or for phenylalanine which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure based studies on iGluR-ligand interactions. PMID:23434404

Asymmetry of the Brain: Development and Implications.

PubMed

Duboc, Véronique; Dufourcq, Pascale; Blader, Patrick; Roussigné, Myriam

2015-01-01

Although the left and right hemispheres of our brains develop with a high degree of symmetry at both the anatomical and functional levels, it has become clear that subtle structural differences exist between the two sides and that each is dominant in processing specific cognitive tasks. As the result of evolutionary conservation or convergence, lateralization of the brain is found in both vertebrates and invertebrates, suggesting that it provides significant fitness for animal life. This widespread feature of hemispheric specialization has allowed the emergence of model systems to study its development and, in some cases, to link anatomical asymmetries to brain function and behavior. Here, we present some of what is known about brain asymmetry in humans and model organisms as well as what is known about the impact of environmental and genetic factors on brain asymmetry development. We specifically highlight the progress made in understanding the development of epithalamic asymmetries in zebrafish and how this model provides an exciting opportunity to address brain asymmetry at different levels of complexity.

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression.

PubMed

Espiritu, Shadrielle Melijah G; Liu, Lydia Y; Rubanova, Yulia; Bhandari, Vinayak; Holgersen, Erle M; Szyca, Lesia M; Fox, Natalie S; Chua, Melvin L K; Yamaguchi, Takafumi N; Heisler, Lawrence E; Livingstone, Julie; Wintersinger, Jeff; Yousif, Fouad; Lalonde, Emilie; Rouette, Alexandre; Salcedo, Adriana; Houlahan, Kathleen E; Li, Constance H; Huang, Vincent; Fraser, Michael; van der Kwast, Theodorus; Morris, Quaid D; Bristow, Robert G; Boutros, Paul C

2018-05-03

The majority of newly diagnosed prostate cancers are slow growing, with a long natural life history. Yet a subset can metastasize with lethal consequences. We reconstructed the phylogenies of 293 localized prostate tumors linked to clinical outcome data. Multiple subclones were detected in 59% of patients, and specific subclonal architectures associate with adverse clinicopathological features. Early tumor development is characterized by point mutations and deletions followed by later subclonal amplifications and changes in trinucleotide mutational signatures. Specific genes are selectively mutated prior to or following subclonal diversification, including MTOR, NKX3-1, and RB1. Patients with low-risk monoclonal tumors rarely relapse after primary therapy (7%), while those with high-risk polyclonal tumors frequently do (61%). The presence of multiple subclones in an index biopsy may be necessary, but not sufficient, for relapse of localized prostate cancer, suggesting that evolution-aware biomarkers should be studied in prospective studies of low-risk tumors suitable for active surveillance. Copyright © 2018 Elsevier Inc. All rights reserved.

Tracing the origin of the panda's thumb

NASA Astrophysics Data System (ADS)

Abella, Juan; Pérez-Ramos, Alejandro; Valenciano, Alberto; Alba, David M.; Ercoli, Marcos D.; Hontecillas, Daniel; Montoya, Plinio; Morales, Jorge

2015-06-01

We investigate the relative development of the carnivoran radial sesamoids to untangle the evolution of this iconic structure. In the pandas (both giant and red), this `false thumb' is known to perform a grasping role during bamboo feeding in both the red and giant pandas. An original locomotor role has been inferred for ailurids, but this remains to be ascertained for ursids. A large sample of radial sesamoids of Indarctos arctoides from the Miocene of Batallones-3 (Spain) indicates that this early ailuropodine bear displayed a relatively hypertrophied radial sesamoid, with a configuration more similar to that of the red panda and other carnivorans than to that of giant pandas. This false thumb is the first evidence of this feature in the Ursidae, which can be linked to a more herbivorous diet. Moreover, in the two extant pandas, the false thumb should not be interpreted as an anatomical convergence, but as an exaptive convergence regarding its use during the bamboo feeding, which changes the evolutionary view of this singular structure.

On the thermodynamic framework of generalized coupled thermoelastic-viscoplastic-damage modeling

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.

1991-01-01

A complete potential based framework using internal state variables is put forth for the derivation of reversible and irreversible constitutive equations. In this framework, the existence of the total (integrated) form of either the (Helmholtz) free energy or the (Gibbs) complementary free energy are assumed a priori. Two options for describing the flow and evolutionary equations are described, wherein option one (the fully coupled form) is shown to be over restrictive while the second option (the decoupled form) provides significant flexibility. As a consequence of the decoupled form, a new operator, i.e., the Compliance operator, is defined which provides a link between the assumed Gibb's and complementary dissipation potential and ensures a number of desirable numerical features, for example the symmetry of the resulting consistent tangent stiffness matrix. An important conclusion reached, is that although many theories in the literature do not conform to the general potential framework outlined, it is still possible in some cases, by slight modifications of the used forms, to restore the complete potential structure.

Structure of human Cdc45 and implications for CMG helicase function

PubMed Central

Simon, Aline C.; Sannino, Vincenzo; Costanzo, Vincenzo; Pellegrini, Luca

2016-01-01

Cell division cycle protein 45 (Cdc45) is required for DNA synthesis during genome duplication, as a component of the Cdc45-MCM-GINS (CMG) helicase. Despite its essential biological function, its biochemical role in DNA replication has remained elusive. Here we report the 2.1-Å crystal structure of human Cdc45, which confirms its evolutionary link with the bacterial RecJ nuclease and reveals several unexpected features that underpin its function in eukaryotic DNA replication. These include a long-range interaction between N- and C-terminal DHH domains, blocking access to the DNA-binding groove of its RecJ-like fold, and a helical insertion in its N-terminal DHH domain, which appears poised for replisome interactions. In combination with available electron microscopy data, we validate by mutational analysis the mechanism of Cdc45 association with the MCM ring and GINS co-activator, critical for CMG assembly. These findings provide an indispensable molecular basis to rationalize the essential role of Cdc45 in genomic duplication. PMID:27189187

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

PubMed Central

Wolf, Maxim Y; Wolf, Yuri I; Koonin, Eugene V

2008-01-01

Background Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. Results This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in multidomain proteins or contained in distinct proteins. Substantial homogenization of evolutionary rates in multidomain proteins was, indeed, observed in both animals and plants, although highly significant differences between domain-specific rates remained. The contributions of the translation rate, as determined by the effect of the fusion of a pair of domains within a multidomain protein, and intrinsic, domain-specific structural-functional constraints appear to be comparable in magnitude. Conclusion Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain. Thus, the rate of translation and intrinsic structural-functional constraints both exert sizable and comparable effects on sequence evolution. Reviewers This article was reviewed by Sergei Maslov, Dennis Vitkup, Claus Wilke (nominated by Orly Alter), and Allan Drummond (nominated by Joel Bader). For the full reviews, please go to the Reviewers' Reports section. PMID:18840284

Linking evolutionary lineage with parasite and pathogen prevalence in the Iberian honey bee.

PubMed

Jara, Laura; Cepero, Almudena; Garrido-Bailón, Encarna; Martín-Hernández, Raquel; Higes, Mariano; De la Rúa, Pilar

2012-05-01

The recent decline in honey bee colonies observed in both European countries and worldwide is of great interest and concern, although the underlying causes remain poorly understood. In recent years, growing evidence has implicated parasites and pathogens in this decline of both the vitality and number of honey bee colonies. The Iberian Peninsula provides an interesting environment in which to study the occurrence of pathogens and parasites in the host honey bee populations due to the presence of two evolutionary lineages in A. m. iberiensis (Western European [M] or African [A]). Here, we provide the first evidence linking the population structure of the Iberian honey bee with the prevalence of some of its most important parasites and pathogens: the Varroa destructor mite and the microsporidia Nosema apis and Nosema ceranae. Using data collected in two surveys conducted in 2006 and 2010 in 41 Spanish provinces, the evolutionary lineage and the presence of the three parasitic organisms cited above were analyzed in a total of 228 colonies. In 2006 N. apis was found in a significantly higher proportion of M lineage honey bees than in the A lineage. However, in 2010 this situation had changed significantly due to a higher prevalence of N. ceranae. We observed no significant relationships in either year between the distributions of V. destructor or N. ceranae and the evolutionary lineage present in A. m. iberiensis colonies, but the effects of these organisms on the genetic diversity of the honey bee populations need further research. Copyright © 2012 Elsevier Inc. All rights reserved.

Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change†

PubMed Central

Xie, Gary; Keyhani, Nemat O.; Bonner; Jensen, Roy A.

2003-01-01

The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting features that can be distinguished. As additional genomes are thoroughly analyzed, an increasingly refined resolution of the sequential evolutionary steps is clearly possible. These comparisons suggest that present-day trp operons that possess finely tuned regulatory features are under strong positive selection and are able to resist the disruptive evolutionary events that may be experienced by simpler, poorly regulated operons. PMID:12966138

Enhanced production of medicinal polysaccharide by submerged fermentation of Lingzhi or Reishi medicinal mushroom Ganoderma lucidium (W.Curt.:Fr.) P. Karst. Using statistical and evolutionary optimization methods.

PubMed

Baskar, Gurunathan; Sathya, Shree Rajesh K

2011-01-01

Statistical and evolutionary optimization of media composition was employed for the production of medicinal exopolysaccharide (EPS) by Lingzhi or Reishi medicinal mushroom Ganoderma lucidium MTCC 1039 using soya bean meal flour as low-cost substrate. Soya bean meal flour, ammonium chloride, glucose, and pH were identified as the most important variables for EPS yield using the two-level Plackett-Burman design and further optimized using the central composite design (CCD) and the artificial neural network (ANN)-linked genetic algorithm (GA). The high value of coefficient of determination of ANN (R² = 0.982) indicates that the ANN model was more accurate than the second-order polynomial model of CCD (R² = 0.91) for representing the effect of media composition on EPS yield. The predicted optimum media composition using ANN-linked GA was soybean meal flour 2.98%, glucose 3.26%, ammonium chloride 0.25%, and initial pH 7.5 for the maximum predicted EPS yield of 1005.55 mg/L. The experimental EPS yield obtained using the predicted optimum media composition was 1012.36 mg/L, which validates the high degree of accuracy of evolutionary optimization for enhanced production of EPS by submerged fermentation of G. lucidium.

Sibship effects on dispersal behaviour in a pre-industrial human population.

PubMed

Nitsch, A; Lummaa, V; Faurie, C

2016-10-01

Understanding dispersal behaviour and its determinants is critical for studies on life-history maximizing strategies. Although many studies have investigated the causes of dispersal, few have focused on the importance of sibship, despite that sibling interactions are predicted to lead to intrafamilial differences in dispersal patterns. Using a large demographic data set from pre-industrial Finland (n = 9000), we tested whether the sex-specific probability of dispersal depended on the presence of same-sex or opposite-sex elder siblings who can both compete and cooperate in the family. Overall, following our predictions, the presence of same-sex elder siblings increased the probability of dispersal from natal population for both sexes, whereas the number of opposite-sex siblings had less influence. Among males, dispersal was strongly linked to access to land resources. Female dispersal was mainly associated with competition over availability of mates but likely mediated by competition over access to wealthy mates rather mate availability per se. Besides ecological constraints, sibling interactions are strongly linked with dispersal decisions and need to be better considered in the studies on the evolution of family dynamics and fitness maximizing strategies in humans and other species. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Informations in Models of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Rivoire, Olivier

2016-03-01

Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of evolutionary dynamics and show how explicit results are obtained for a solvable subclass of these models. In several limits, the results coincide with those obtained in studies of information processing for communication, gambling or thermodynamics. In the most general case, however, information processing by biological populations shows unique features that motivate the analysis of specific models.

Possible steps in the evolutionary development of bird navigation

NASA Technical Reports Server (NTRS)

Bellrose, F. C.

1972-01-01

Hypotheses are presented to explain the evolutionary development of navigational ability in migratory birds. Areas of discussion to describe the possible techniques are: (1) sun compass, (2) bicoordinate navigation, (3) star compass, (4) wind cues, (5) earth magnetic field, and (6) landscape features. It is concluded that landscape is the single most important cue for orientation of nonmigratory birds. The long range migratory birds appear to use a combination of cues with the relative importance of the cue dependent upon the species of the bird involved.

The role of habitat choice in micro-evolutionary dynamics: An experimental study on the Mediterranean killifish Aphanius fasciatus (Cyprinodontidae).

PubMed

Angeletti, Dario; Sebbio, Claudia; Carlini, Alessandro; Strinati, Claudia; Nascetti, Giuseppe; Carere, Claudio; Cimmaruta, Roberta

2017-12-01

Habitat choice is defined as a nonrandom distribution of genotypes in different microhabitats. Therefore, it could exert a great impact on the genetic variance of natural populations by promoting genetic divergence, local adaptation, and may even lead to sympatric speciation. Despite this potential role in micro- and macro-evolutionary processes, there is little empirical evidence that the various genotypes within a population may differ in habitat choice-related behaviors. Here, we tested whether habitat choice may have contributed to genetic divergence within a local population of the Mediterranean killifish Aphanius fasciatus , which emerged between groups inhabiting microhabitats with different oxygen concentrations during previous field studies. In a first experiment, we studied the distribution of individuals in conditions of hypoxia and normoxia to test whether they had a different ability to shy away from a hypoxic environment; in a second experiment, we analyzed the individual behavior of fish separately in the two conditions, to verify whether they showed peculiar behavioral responses linked to a possible differential distribution. We then analyzed the six allozyme loci, whose allelic and genotypic frequencies were significantly divergent in the previous studies. In the first test, we found that the distribution of the two homozygote genotypes of the glucose-6-phosphate isomerase-1 locus (GPI-1) was significantly different between the hypoxic and the normoxic conditions. During the second test, all individuals were more active in hypoxic conditions, but the two GPI-1 homozygotes showed a significant difference in time spent performing surface breathing, which was consistent with their distribution observed in the first experiment. These results provide evidence that individual behavioral traits, related to genetic features, may lead to a nonrandom distribution of genotypes in heterogeneous although contiguous microhabitats and, consequently, that habitat choice can play a significant role in driving the micro-evolutionary dynamics of this species.

Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella.

PubMed

Harms, Alexander; Segers, Francisca H I D; Quebatte, Maxime; Mistl, Claudia; Manfredi, Pablo; Körner, Jonas; Chomel, Bruno B; Kosoy, Michael; Maruyama, Soichi; Engel, Philipp; Dehio, Christoph

2017-03-01

The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Adaptive evolution of Mediterranean pines.

PubMed

Grivet, Delphine; Climent, José; Zabal-Aguirre, Mario; Neale, David B; Vendramin, Giovanni G; González-Martínez, Santiago C

2013-09-01

Mediterranean pines represent an extremely heterogeneous assembly. Although they have evolved under similar environmental conditions, they diversified long ago, ca. 10 Mya, and present distinct biogeographic and demographic histories. Therefore, it is of special interest to understand whether and to what extent they have developed specific strategies of adaptive evolution through time and space. To explore evolutionary patterns, the Mediterranean pines' phylogeny was first reconstructed analyzing a new set of 21 low-copy nuclear genes with multilocus Bayesian tree reconstruction methods. Secondly, a phylogenetic approach was used to search for footprints of natural selection and to examine the evolution of multiple phenotypic traits. We identified two genes (involved in pines' defense and stress responses) that have likely played a role in the adaptation of Mediterranean pines to their environment. Moreover, few life-history traits showed historical or evolutionary adaptive convergence in Mediterranean lineages, while patterns of character evolution revealed various evolutionary trade-offs linking growth-development, reproduction and fire-related traits. Assessing the evolutionary path of important life-history traits, as well as the genomic basis of adaptive variation is central to understanding the past evolutionary success of Mediterranean pines and their future response to environmental changes. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolutionary optimization of radial basis function classifiers for data mining applications.

PubMed

Buchtala, Oliver; Klimek, Manuel; Sick, Bernhard

2005-10-01

In many data mining applications that address classification problems, feature and model selection are considered as key tasks. That is, appropriate input features of the classifier must be selected from a given (and often large) set of possible features and structure parameters of the classifier must be adapted with respect to these features and a given data set. This paper describes an evolutionary algorithm (EA) that performs feature and model selection simultaneously for radial basis function (RBF) classifiers. In order to reduce the optimization effort, various techniques are integrated that accelerate and improve the EA significantly: hybrid training of RBF networks, lazy evaluation, consideration of soft constraints by means of penalty terms, and temperature-based adaptive control of the EA. The feasibility and the benefits of the approach are demonstrated by means of four data mining problems: intrusion detection in computer networks, biometric signature verification, customer acquisition with direct marketing methods, and optimization of chemical production processes. It is shown that, compared to earlier EA-based RBF optimization techniques, the runtime is reduced by up to 99% while error rates are lowered by up to 86%, depending on the application. The algorithm is independent of specific applications so that many ideas and solutions can be transferred to other classifier paradigms.

Common position of indels that cause deviations from canonical genome organization in different measles virus strains.

PubMed

Ivancic-Jelecki, Jelena; Slovic, Anamarija; Šantak, Maja; Tešović, Goran; Forcic, Dubravko

2016-07-29

The canonical genome organization of measles virus (MV) is characterized by total size of 15 894 nucleotides (nts) and defined length of every genomic region, both coding and non-coding. Only rarely have reports of strains possessing non-canonical genomic properties (possessing indels, with or without the change of total genome length) been published. The observed mutations are mutually compensatory in a sense that the total genome length remains polyhexameric. Although programmed and highly precise pseudo-templated nucleotide additions during transcription are inherent to polymerases of all viruses belonging to family Paramyxoviridae, a similar mechanism that would serve to non-randomly correct genome length, if an indel has occurred during replication, has so far not been described in the context of a complete virus genome. We compiled all complete MV genomic sequences (64 in total) available in open access sequence databases. Multiple sequence comparisons and phylogenetic analyses were performed with the aim of exploring whether non-recombinant and non-evolutionary linked measles strains that show deviations from canonical genome organization possess a common genetic characteristic. In 11 MV sequences we detected deviations from canonical genome organization due to short indels located within homopolymeric stretches or next to them. In nine out of 11 identified non-canonical MV sequences, a common feature was observed: one mutation, either an insertion or a deletion, was located in a 28 nts long region in F gene 5' untranslated region (positions 5051-5078 in genomic cDNA of canonical strains). This segment is composed of five tandemly linked homopolymeric stretches, its consensus sequence is G6-7C7-8A6-7G1-3C5-6. Although none of the mononucleotide repeats within this segment has fixed length, the total number of nts in canonical strains is always 28. These nine non-canonical strains, as well as the tenth (not mutated in 5051-5078 segment), can be grouped in three clusters, based on their passage histories/epidemiological data/genetic similarities. There are no indications that the 3 clusters are evolutionary linked, other than the fact that they all belong to clade D. A common narrow genomic region was found to be mutated in different, non-related, wild type strains suggesting that this region might have a function in non-random genome length corrections occurring during MV replication.

Using HexSim to link demography and genetics in animal and plant simulations

EPA Science Inventory

Simulation models are essential for understanding the effects of land management practices and environmental drivers, including landscape change, shape population genetic structure and persistence probabilities. The emerging field of eco-evolutionary modeling is beginning to dev...

ECOD: An Evolutionary Classification of Protein Domains

PubMed Central

Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V.

2014-01-01

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies. PMID:25474468

ECOD: an evolutionary classification of protein domains.

PubMed

Cheng, Hua; Schaeffer, R Dustin; Liao, Yuxing; Kinch, Lisa N; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V

2014-12-01

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or "fold"). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.

An evolutionary advantage for extravagant honesty.

PubMed

Bullock, Seth

2012-01-07

A game-theoretic model of handicap signalling over a pair of signalling channels is introduced in order to determine when one channel has an evolutionary advantage over the other. The stability conditions for honest handicap signalling are presented for a single channel and are shown to conform with the results of prior handicap signalling models. Evolutionary simulations are then used to show that, for a two-channel system in which honest signalling is possible on both channels, the channel featuring larger advertisements at equilibrium is favoured by evolution. This result helps to address a significant tension in the handicap principle literature. While the original theory was motivated by the prevalence of extravagant natural signalling, contemporary models have demonstrated that it is the cost associated with deception that stabilises honesty, and that the honest signals exhibited at equilibrium need not be extravagant at all. The current model suggests that while extravagant and wasteful signals are not required to ensure a signalling system's evolutionary stability, extravagant signalling systems may enjoy an advantage in terms of evolutionary attainability. Copyright © 2011 Elsevier Ltd. All rights reserved.

A biogeographic network reveals evolutionary links between deep-sea hydrothermal vent and methane seep faunas

PubMed Central

2016-01-01

Deep-sea hydrothermal vents and methane seeps are inhabited by members of the same higher taxa but share few species, thus scientists have long sought habitats or regions of intermediate character that would facilitate connectivity among these habitats. Here, a network analysis of 79 vent, seep, and whale-fall communities with 121 genus-level taxa identified sedimented vents as a main intermediate link between the two types of ecosystems. Sedimented vents share hot, metal-rich fluids with mid-ocean ridge-type vents and soft sediment with seeps. Such sites are common along the active continental margins of the Pacific Ocean, facilitating connectivity among vent/seep faunas in this region. By contrast, sedimented vents are rare in the Atlantic Ocean, offering an explanation for the greater distinction between its vent and seep faunas compared with those of the Pacific Ocean. The distribution of subduction zones and associated back-arc basins, where sedimented vents are common, likely plays a major role in the evolutionary and biogeographic connectivity of vent and seep faunas. The hypothesis that decaying whale carcasses are dispersal stepping stones linking these environments is not supported. PMID:27974524

Missing links: the genetic architecture of flowers [correction of flower] and floral diversification.

PubMed

Soltis, Douglas E; Soltis, Pamela S; Albert, Victor A; Oppenheimer, David G; dePamphilis, Claude W; Ma, Hong; Frohlich, Michael W; Theissen, Günter

2002-01-01

To understand the genetic architecture of floral development, including the origin and subsequent diversification of the flower, data are needed not only for a few model organisms but also for gymnosperms, basal angiosperm lineages and early-diverging eudicots. We must link what is known about derived model plants such as Arabidopsis, snapdragon and maize with other angiosperms. To this end, we suggest a massive evolutionary genomics effort focused on the identification and expression patterns of floral genes and elucidation of their expression patterns in 'missing-link' taxa differing in the arrangement, number and organization of floral parts.

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx

PubMed Central

Stenseth, Nils Chr.; Ehrich, Dorothee; Rueness, Eli Knispel; Lingjærde, Ole Chr.; Chan, Kung-Sik; Boutin, Stan; O'Donoghue, Mark; Robinson, David A.; Viljugrein, Hildegunn; Jakobsen, Kjetill S.

2004-01-01

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the “climate forcing of ecological and evolutionary patterns” model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics. PMID:15067131

Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

NASA Astrophysics Data System (ADS)

Xing, Yuanzhi; Deng, Xiaoyi

2017-11-01

The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

A possible biochemical missing link among archaebacteria

NASA Technical Reports Server (NTRS)

Achenbach-Richter, Laurie; Woese, Carl R.; Stetter, Karl O.

1987-01-01

The characteristics of the newly discovered strain of archaebacteria, VC-16, the only archaebacterium known to reduce sulfate, suggest that VC-16 might represent a transitional form between an anaerobic thermophilic sulfur-based type of metabolism and methanogenesis. It is shown here, using a matrix of evolutionary distances derived from an alignment of various archaebacterial 16S rRNAs and the phylogenetic tree derived from these evolutionary distances, that the lineage represented by strain VC-16 arises from the archaebacterial tree precisely where such an interpretation would predict that it would, between the Methanococcus lineage and that of Thermococcus.

Why an extended evolutionary synthesis is necessary

PubMed Central

2017-01-01

Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology. PMID:28839929

Empirical verification of evolutionary theories of aging.

PubMed

Kyryakov, Pavlo; Gomez-Perez, Alejandra; Glebov, Anastasia; Asbah, Nimara; Bruno, Luigi; Meunier, Carolynne; Iouk, Tatiana; Titorenko, Vladimir I

2016-10-25

We recently selected 3 long-lived mutant strains of Saccharomyces cerevisiae by a lasting exposure to exogenous lithocholic acid. Each mutant strain can maintain the extended chronological lifespan after numerous passages in medium without lithocholic acid. In this study, we used these long-lived yeast mutants for empirical verification of evolutionary theories of aging. We provide evidence that the dominant polygenic trait extending longevity of each of these mutants 1) does not affect such key features of early-life fitness as the exponential growth rate, efficacy of post-exponential growth and fecundity; and 2) enhances such features of early-life fitness as susceptibility to chronic exogenous stresses, and the resistance to apoptotic and liponecrotic forms of programmed cell death. These findings validate evolutionary theories of programmed aging. We also demonstrate that under laboratory conditions that imitate the process of natural selection within an ecosystem, each of these long-lived mutant strains is forced out of the ecosystem by the parental wild-type strain exhibiting shorter lifespan. We therefore concluded that yeast cells have evolved some mechanisms for limiting their lifespan upon reaching a certain chronological age. These mechanisms drive the evolution of yeast longevity towards maintaining a finite yeast chronological lifespan within ecosystems.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

PubMed

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

Early Cambrian sipunculan worms from southwest China.

PubMed Central

Huang, Di-Ying; Chen, Jun-Yuan; Vannier, Jean; Saiz Salinas, J. I.

2004-01-01

We report the discovery of sipunculan worms from the Lower Cambrian Maotianshan Shale, near Kunming (southwest China). Their sipunculan identity is evidenced by the general morphology of the animals (sausage-shaped body with a slender retractable introvert and a wider trunk) and by other features, both external (e.g. perioral crown of tentacles, and hooks, papillae and wrinkle rings on the body surface) and internal (U-shaped gut, and the anus opening near the introvert-trunk junction). The three fossil forms (Archaeogolfingia caudata gen. et sp. nov., Cambrosipunculus tentaculatus gen. et sp. nov. and Cambrosipunculus sp.) have striking similarities to modern sipunculans, especially the Golfingiidae to which their evolutionary relationships are discussed. This study suggests that most typical features of extant sipunculans have undergone only limited changes since the Early Cambrian, thus indicating a possible evolutionary stasis over the past 520 Myr. PMID:15306286

Early Cambrian sipunculan worms from southwest China.

PubMed

Huang, Di-Ying; Chen, Jun-Yuan; Vannier, Jean; Saiz Salinas, J I

2004-08-22

We report the discovery of sipunculan worms from the Lower Cambrian Maotianshan Shale, near Kunming (southwest China). Their sipunculan identity is evidenced by the general morphology of the animals (sausage-shaped body with a slender retractable introvert and a wider trunk) and by other features, both external (e.g. perioral crown of tentacles, and hooks, papillae and wrinkle rings on the body surface) and internal (U-shaped gut, and the anus opening near the introvert-trunk junction). The three fossil forms (Archaeogolfingia caudata gen. et sp. nov., Cambrosipunculus tentaculatus gen. et sp. nov. and Cambrosipunculus sp.) have striking similarities to modern sipunculans, especially the Golfingiidae to which their evolutionary relationships are discussed. This study suggests that most typical features of extant sipunculans have undergone only limited changes since the Early Cambrian, thus indicating a possible evolutionary stasis over the past 520 Myr.

Configurable pattern-based evolutionary biclustering of gene expression data

PubMed Central

2013-01-01

Background Biclustering algorithms for microarray data aim at discovering functionally related gene sets under different subsets of experimental conditions. Due to the problem complexity and the characteristics of microarray datasets, heuristic searches are usually used instead of exhaustive algorithms. Also, the comparison among different techniques is still a challenge. The obtained results vary in relevant features such as the number of genes or conditions, which makes it difficult to carry out a fair comparison. Moreover, existing approaches do not allow the user to specify any preferences on these properties. Results Here, we present the first biclustering algorithm in which it is possible to particularize several biclusters features in terms of different objectives. This can be done by tuning the specified features in the algorithm or also by incorporating new objectives into the search. Furthermore, our approach bases the bicluster evaluation in the use of expression patterns, being able to recognize both shifting and scaling patterns either simultaneously or not. Evolutionary computation has been chosen as the search strategy, naming thus our proposal Evo-Bexpa (Evolutionary Biclustering based in Expression Patterns). Conclusions We have conducted experiments on both synthetic and real datasets demonstrating Evo-Bexpa abilities to obtain meaningful biclusters. Synthetic experiments have been designed in order to compare Evo-Bexpa performance with other approaches when looking for perfect patterns. Experiments with four different real datasets also confirm the proper performing of our algorithm, whose results have been biologically validated through Gene Ontology. PMID:23433178

Developmental and Evolutionary History Affect Survival in Stressful Environments

PubMed Central

Hopkins, Gareth R.; Brodie, Edmund D.; French, Susannah S.

2014-01-01

The world is increasingly impacted by a variety of stressors that have the potential to differentially influence life history stages of organisms. Organisms have evolved to cope with some stressors, while with others they have little capacity. It is thus important to understand the effects of both developmental and evolutionary history on survival in stressful environments. We present evidence of the effects of both developmental and evolutionary history on survival of a freshwater vertebrate, the rough-skinned newt (Taricha granulosa) in an osmotically stressful environment. We compared the survival of larvae in either NaCl or MgCl2 that were exposed to salinity either as larvae only or as embryos as well. Embryonic exposure to salinity led to greater mortality of newt larvae than larval exposure alone, and this reduced survival probability was strongly linked to the carry-over effect of stunted embryonic growth in salts. Larval survival was also dependent on the type of salt (NaCl or MgCl2) the larvae were exposed to, and was lowest in MgCl2, a widely-used chemical deicer that, unlike NaCl, amphibian larvae do not have an evolutionary history of regulating at high levels. Both developmental and evolutionary history are critical factors in determining survival in this stressful environment, a pattern that may have widespread implications for the survival of animals increasingly impacted by substances with which they have little evolutionary history. PMID:24748021

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2018-05-01

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Sex Differences in Impulsivity: A Meta-Analysis

ERIC Educational Resources Information Center

Cross, Catharine P.; Copping, Lee T.; Campbell, Anne

2011-01-01

Men are overrepresented in socially problematic behaviors, such as aggression and criminal behavior, which have been linked to impulsivity. Our review of impulsivity is organized around the tripartite theoretical distinction between reward hypersensitivity, punishment hyposensitivity, and inadequate effortful control. Drawing on evolutionary,…

Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants.

PubMed

Hunt, Arthur G; Xing, Denghui; Li, Qingshun Q

2012-11-20

Polyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors. The polyadenylation factors are largely conserved across mammals and fungi. The conservation seems also extended to plants based on the analyses of Arabidopsis polyadenylation factors. To extend this observation, we systemically identified the orthologs of yeast and human polyadenylation factors from 10 plant species chosen based on both the availability of their genome sequences and their positions in the evolutionary tree, which render them representatives of different plant lineages. The evolutionary trajectories revealed several interesting features of plant polyadenylation factors. First, the number of genes encoding plant polyadenylation factors was clearly increased from "lower" to "higher" plants. Second, the gene expansion in higher plants was biased to some polyadenylation factors, particularly those involved in RNA binding. Finally, while there are clear commonalities, the differences in the polyadenylation apparatus were obvious across different species, suggesting an ongoing process of evolutionary change. These features lead to a model in which the plant polyadenylation complex consists of a conserved core, which is rather rigid in terms of evolutionary conservation, and a panoply of peripheral subunits, which are less conserved and associated with the core in various combinations, forming a collection of somewhat distinct complex assemblies. The multiple forms of plant polyadenylation complex, together with the diversified polyA signals may explain the intensive alternative polyadenylation (APA) and its regulatory role in biological functions of higher plants.

Crassulacean Acid Metabolism and Epiphytism Linked to Adaptive Radiations in the Orchidaceae1[OA

PubMed Central

Silvera, Katia; Santiago, Louis S.; Cushman, John C.; Winter, Klaus

2009-01-01

Species of the large family Orchidaceae display a spectacular array of adaptations and rapid speciations that are linked to several innovative features, including specialized pollination syndromes, colonization of epiphytic habitats, and the presence of Crassulacean acid metabolism (CAM), a water-conserving photosynthetic pathway. To better understand the role of CAM and epiphytism in the evolutionary expansion of tropical orchids, we sampled leaf carbon isotopic composition of 1,103 species native to Panama and Costa Rica, performed character state reconstruction and phylogenetic trait analysis of CAM and epiphytism, and related strong CAM, present in 10% of species surveyed, to climatic variables and the evolution of epiphytism in tropical regions. Altitude was the most important predictor of photosynthetic pathway when all environmental variables were taken into account, with CAM being most prevalent at low altitudes. By creating integrated orchid trees to reconstruct ancestral character states, we found that C3 photosynthesis is the ancestral state and that CAM has evolved at least 10 independent times with several reversals. A large CAM radiation event within the Epidendroideae, the most species-rich epiphytic clade of any known plant group, is linked to a Tertiary species radiation that originated 65 million years ago. Our study shows that parallel evolution of CAM is present among subfamilies of orchids, and correlated divergence between photosynthetic pathways and epiphytism can be explained by the prevalence of CAM in low-elevation epiphytes and rapid speciation of high-elevation epiphytes in the Neotropics, contributing to the astounding diversity in the Orchidaceae. PMID:19182098

Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors.

PubMed

M Oziolor, Elias; De Schamphelaere, Karel; Matson, Cole W

2016-12-01

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks.

Feature Selection in Classification of Eye Movements Using Electrooculography for Activity Recognition

PubMed Central

Mala, S.; Latha, K.

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition. PMID:25574185

Feature selection in classification of eye movements using electrooculography for activity recognition.

PubMed

Mala, S; Latha, K

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition.

Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding.

PubMed

Forstmeier, W; Ihle, M; Opatová, P; Martin, K; Knief, U; Albrechtová, J; Albrecht, T; Kempenaers, B

2017-05-01

The phenotype-linked fertility hypothesis suggests that females can judge male fertility by inspecting male phenotypic traits. This is because male sexually selected traits might correlate with sperm quality if both are sensitive to factors that influence male condition. A recent meta-analysis found little support for this hypothesis, suggesting little or no shared condition dependence. However, we recently reported that in captive zebra finches (Taeniopygia guttata) inbreeding had detrimental effects both on phenotypic traits and on measures of sperm quality, implying that variation in inbreeding could induce positive covariance between indicator traits and sperm quality. Therefore, we here assess empirically the average strength of correlations between phenotypic traits (courtship rate, beak colour, tarsus length) and measures of sperm quality (proportion of functional sperm, sperm velocity, sperm length) in populations of only outbred individuals and in mixed populations consisting of inbreds (F = 0.25) and outbreds (F = 0). As expected, phenotype sperm-trait correlations were stronger when the population contained a mix of inbred and outbred individuals. We also found unexpected heterogeneity between our two study populations, with correlations being considerably stronger in a domesticated population than in a recently wild-derived population. Correlations ranged from essentially zero among outbred-only wild-derived birds (mean Fisher's Zr ± SE = 0.03 ± 0.10) to moderately strong among domesticated birds of mixed inbreeding status (Zr ± SE = 0.38 ± 0.08). Our results suggest that, under some conditions, the phenotype-linked fertility hypothesis might apply. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

PubMed

Guo, Yue; Liu, Jing; Zhang, Jiefu; Liu, Shengyi; Du, Jianchang

2017-07-01

It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K a ) and the rates of synonymous substitution (K s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K a /K s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Bistability of Evolutionary Stable Vaccination Strategies in the Reinfection SIRI Model.

PubMed

Martins, José; Pinto, Alberto

2017-04-01

We use the reinfection SIRI epidemiological model to analyze the impact of education programs and vaccine scares on individuals decisions to vaccinate or not. The presence of the reinfection provokes the novelty of the existence of three Nash equilibria for the same level of the morbidity relative risk instead of a single Nash equilibrium as occurs in the SIR model studied by Bauch and Earn (PNAS 101:13391-13394, 2004). The existence of three Nash equilibria, with two of them being evolutionary stable, introduces two scenarios with relevant and opposite features for the same level of the morbidity relative risk: the low-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a low probability; and the high-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a high probability. We introduce the evolutionary vaccination dynamics for the SIRI model and we prove that it is bistable. The bistability of the evolutionary dynamics indicates that the damage provoked by false scares on the vaccination perceived morbidity risks can be much higher and much more persistent than in the SIR model. Furthermore, the vaccination education programs to be efficient they need to implement a mechanism to suddenly increase the vaccination coverage level.

Making evolutionary history count: biodiversity planning for coral reef fishes and the conservation of evolutionary processes

NASA Astrophysics Data System (ADS)

von der Heyden, Sophie

2017-03-01

Anthropogenic activities are having devastating impacts on marine systems with numerous knock-on effects on trophic functioning, species interactions and an accelerated loss of biodiversity. Establishing conservation areas can not only protect biodiversity, but also confer resilience against changes to coral reefs and their inhabitants. Planning for protection and conservation in marine systems is complex, but usually focuses on maintaining levels of biodiversity and protecting special and unique landscape features while avoiding negative impacts to socio-economic benefits. Conversely, the integration of evolutionary processes that have shaped extant species assemblages is rarely taken into account. However, it is as important to protect processes as it is to protect patterns for maintaining the evolutionary trajectories of populations and species. This review focuses on different approaches for integrating genetic analyses, such as phylogenetic diversity, phylogeography and the delineation of management units, temporal and spatial monitoring of genetic diversity and quantification of adaptive variation for protecting evolutionary resilience, into marine spatial planning, specifically for coral reef fishes. Many of these concepts are not yet readily applied to coral reef fish studies, but this synthesis highlights their potential and the importance of including historical processes into systematic biodiversity planning for conserving not only extant, but also future, biodiversity and its evolutionary potential.

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

PubMed Central

Ashkenazy, Haim; Abadi, Shiran; Martz, Eric; Chay, Ofer; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir

2016-01-01

The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree. PMID:27166375

Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

PubMed

Glinsky, Gennadi V

2018-03-01

Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.

Conservation of transcription factor binding events predicts gene expression across species

PubMed Central

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

Natural Selection in Large Populations

NASA Astrophysics Data System (ADS)

Desai, Michael

2011-03-01

I will discuss theoretical and experimental approaches to the evolutionary dynamics and population genetics of natural selection in large populations. In these populations, many mutations are often present simultaneously, and because recombination is limited, selection cannot act on them all independently. Rather, it can only affect whole combinations of mutations linked together on the same chromosome. Methods common in theoretical population genetics have been of limited utility in analyzing this coupling between the fates of different mutations. In the past few years it has become increasingly clear that this is a crucial gap in our understanding, as sequence data has begun to show that selection appears to act pervasively on many linked sites in a wide range of populations, including viruses, microbes, Drosophila, and humans. I will describe approaches that combine analytical tools drawn from statistical physics and dynamical systems with traditional methods in theoretical population genetics to address this problem, and describe how experiments in budding yeast can help us directly observe these evolutionary dynamics.

Evolutionary speed limited by water in arid Australia

PubMed Central

Goldie, Xavier; Gillman, Len; Crisp, Mike; Wright, Shane

2010-01-01

The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns. PMID:20410038

Evolutionary speed limited by water in arid Australia.

PubMed

Goldie, Xavier; Gillman, Len; Crisp, Mike; Wright, Shane

2010-09-07

The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns.

Evolutionary potential of marine phytoplankton under ocean acidification.

PubMed

Collins, Sinéad; Rost, Björn; Rynearson, Tatiana A

2014-01-01

Marine phytoplankton have many obvious characters, such as rapid cell division rates and large population sizes, that give them the capacity to evolve in response to global change on timescales of weeks, months or decades. However, few studies directly investigate if this adaptive potential is likely to be realized. Because of this, evidence of to whether and how marine phytoplankton may evolve in response to global change is sparse. Here, we review studies that help predict evolutionary responses to global change in marine phytoplankton. We find limited support from experimental evolution that some taxa of marine phytoplankton may adapt to ocean acidification, and strong indications from studies of variation and structure in natural populations that selection on standing genetic variation is likely. Furthermore, we highlight the large body of literature on plastic responses to ocean acidification available, and evolutionary theory that may be used to link plastic and evolutionary responses. Because of the taxonomic breadth spanned by marine phytoplankton, and the diversity of roles they fill in ocean ecosystems and biogeochemical cycles, we stress the necessity of treating taxa or functional groups individually.

Phylogenetic context determines the role of competition in adaptive radiation

PubMed Central

Tan, Jiaqi; Slattery, Matthew R.; Yang, Xian; Jiang, Lin

2016-01-01

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes. PMID:27335414

An open future for ecological and evolutionary data?

PubMed

Kenall, Amye; Harold, Simon; Foote, Christopher

2014-04-02

As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.

Hybrid evolutionary computing model for mobile agents of wireless Internet multimedia

NASA Astrophysics Data System (ADS)

Hortos, William S.

2001-03-01

The ecosystem is used as an evolutionary paradigm of natural laws for the distributed information retrieval via mobile agents to allow the computational load to be added to server nodes of wireless networks, while reducing the traffic on communication links. Based on the Food Web model, a set of computational rules of natural balance form the outer stage to control the evolution of mobile agents providing multimedia services with a wireless Internet protocol WIP. The evolutionary model shows how mobile agents should behave with the WIP, in particular, how mobile agents can cooperate, compete and learn from each other, based on an underlying competition for radio network resources to establish the wireless connections to support the quality of service QoS of user requests. Mobile agents are also allowed to clone themselves, propagate and communicate with other agents. A two-layer model is proposed for agent evolution: the outer layer is based on the law of natural balancing, the inner layer is based on a discrete version of a Kohonen self-organizing feature map SOFM to distribute network resources to meet QoS requirements. The former is embedded in the higher OSI layers of the WIP, while the latter is used in the resource management procedures of Layer 2 and 3 of the protocol. Algorithms for the distributed computation of mobile agent evolutionary behavior are developed by adding a learning state to the agent evolution state diagram. When an agent is in an indeterminate state, it can communicate to other agents. Computing models can be replicated from other agents. Then the agents transitions to the mutating state to wait for a new information-retrieval goal. When a wireless terminal or station lacks a network resource, an agent in the suspending state can change its policy to submit to the environment before it transitions to the searching state. The agents learn the facts of agent state information entered into an external database. In the cloning process, two agents on a host station sharing a common goal can be merged or married to compose a new agent. Application of the two-layer set of algorithms for mobile agent evolution, performed in a distributed processing environment, is made to the QoS management functions of the IP multimedia IM sub-network of the third generation 3G Wideband Code-division Multiple Access W-CDMA wireless network.

Coexistence of fraternity and egoism for spatial social dilemmas.

PubMed

Szabó, György; Szolnoki, Attila; Czakó, Lilla

2013-01-21

We have studied an evolutionary game with spatially arranged players who can choose one of the two strategies (named cooperation and defection for social dilemmas) when playing with their neighbors. In addition to the application of the usual strategies in the present model the players are also characterized by one of the two extreme personal features representing the egoist or fraternal behavior. During the evolution each player can modify both her own strategy and/or personal feature via a myopic update process in order to improve her utility. The results of numerical simulations and stability analysis are summarized in phase diagrams representing a wide scale of spatially ordered distribution of strategies and personal features when varying the payoff parameters. In most of the cases only two of the four possible options prevail and may form sublattice ordered spatial structure. The evolutionary advantage of the fraternal attitude is demonstrated within a large range of payoff parameters including the region of prisoner's dilemma where egoist defectors and fraternal cooperators form a role-separating chessboard like pattern. Copyright © 2012 Elsevier Ltd. All rights reserved.

Endosymbiosis and its implications for evolutionary theory.

PubMed

O'Malley, Maureen A

2015-08-18

Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics "follows" genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation.

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

PubMed

Turajlic, Samra; Xu, Hang; Litchfield, Kevin; Rowan, Andrew; Horswell, Stuart; Chambers, Tim; O'Brien, Tim; Lopez, Jose I; Watkins, Thomas B K; Nicol, David; Stares, Mark; Challacombe, Ben; Hazell, Steve; Chandra, Ashish; Mitchell, Thomas J; Au, Lewis; Eichler-Jonsson, Claudia; Jabbar, Faiz; Soultati, Aspasia; Chowdhury, Simon; Rudman, Sarah; Lynch, Joanna; Fernando, Archana; Stamp, Gordon; Nye, Emma; Stewart, Aengus; Xing, Wei; Smith, Jonathan C; Escudero, Mickael; Huffman, Adam; Matthews, Nik; Elgar, Greg; Phillimore, Ben; Costa, Marta; Begum, Sharmin; Ward, Sophia; Salm, Max; Boeing, Stefan; Fisher, Rosalie; Spain, Lavinia; Navas, Carolina; Grönroos, Eva; Hobor, Sebastijan; Sharma, Sarkhara; Aurangzeb, Ismaeel; Lall, Sharanpreet; Polson, Alexander; Varia, Mary; Horsfield, Catherine; Fotiadis, Nicos; Pickering, Lisa; Schwarz, Roland F; Silva, Bruno; Herrero, Javier; Luscombe, Nick M; Jamal-Hanjani, Mariam; Rosenthal, Rachel; Birkbak, Nicolai J; Wilson, Gareth A; Pipek, Orsolya; Ribli, Dezso; Krzystanek, Marcin; Csabai, Istvan; Szallasi, Zoltan; Gore, Martin; McGranahan, Nicholas; Van Loo, Peter; Campbell, Peter; Larkin, James; Swanton, Charles

2018-04-19

The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of driver event ordering, co-occurrence, and mutual exclusivity at clone level, we show the deterministic nature of clonal evolution. ccRCC can be grouped into seven evolutionary subtypes, ranging from tumors characterized by early fixation of multiple mutational and copy number drivers and rapid metastases to highly branched tumors with >10 subclonal drivers and extensive parallel evolution associated with attenuated progression. We identify genetic diversity and chromosomal complexity as determinants of patient outcome. Our insights reconcile the variable clinical behavior of ccRCC and suggest evolutionary potential as a biomarker for both intervention and surveillance. Copyright © 2018 Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

Evolutionary Dynamics and Diversity in Microbial Populations

NASA Astrophysics Data System (ADS)

Thompson, Joel; Fisher, Daniel

2013-03-01

Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

An evolutionary solution to anesthesia automated record keeping.

PubMed

Bicker, A A; Gage, J S; Poppers, P J

1998-08-01

In the course of five years the development of an automated anesthesia record keeper has evolved through nearly a dozen stages, each marked by new features and sophistication. Commodity PC hardware and software minimized development costs. Object oriented analysis, programming and design supported the process of change. In addition, we developed an evolutionary strategy that optimized motivation, risk management, and maximized return on investment. Besides providing record keeping services, the system supports educational and research activities and through a flexible plotting paradigm, supports each anesthesiologist's focus on physiological data during and after anesthesia.

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanitamore » fungi. We used methods developed to interrogate both assembled and unassembled sequences, and characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.« less

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

DOE PAGES

Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.; ...

2014-06-12

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanitamore » fungi. We used methods developed to interrogate both assembled and unassembled sequences, and characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.« less

Patterns and Processes of Vertebrate Evolution

NASA Astrophysics Data System (ADS)

Carroll, Robert Lynn

1997-04-01

This new text provides an integrated view of the forces that influence the patterns and rates of vertebrate evolution from the level of living populations and species to those that resulted in the origin of the major vertebrate groups. The evolutionary roles of behavior, development, continental drift, and mass extinctions are compared with the importance of variation and natural selection that were emphasized by Darwin. It is extensively illustrated, showing major transitions between fish and amphibians, dinosaurs and birds, and land mammals to whales. No book since Simpson's Major Features of Evolution has attempted such a broad study of the patterns and forces of evolutionary change. Undergraduate students taking a general or advanced course on evolution, and graduate students and professionals in evolutionary biology and paleontology will find the book of great interest.

Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

PubMed Central

Zardus, John D.; Wares, John P.

2016-01-01

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria. PMID:27231653

Evolutionary developmental pathology and anthropology: A new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine.

PubMed

Diogo, Rui; Smith, Christopher M; Ziermann, Janine M

2015-11-01

We introduce a new subfield of the recently created field of Evolutionary-Developmental-Anthropology (Evo-Devo-Anth): Evolutionary-Developmental-Pathology-and-Anthropology (Evo-Devo-P'Anth). This subfield combines experimental and developmental studies of nonhuman model organisms, biological anthropology, chordate comparative anatomy and evolution, and the study of normal and pathological human development. Instead of focusing on other organisms to try to better understand human development, evolution, anatomy, and pathology, it places humans as the central case study, i.e., as truly model organism themselves. We summarize the results of our recent Evo-Devo-P'Anth studies and discuss long-standing questions in each of the broader biological fields combined in this subfield, paying special attention to the links between: (1) Human anomalies and variations, nonpentadactyly, homeotic transformations, and "nearest neighbor" vs. "find and seek" muscle-skeleton associations in limb+facial muscles vs. other head muscles; (2) Developmental constraints, the notion of "phylotypic stage," internalism vs. externalism, and the "logic of monsters" vs. "lack of homeostasis" views about human birth defects; (3) Human evolution, reversions, atavisms, paedomorphosis, and peromorphosis; (4) Scala naturae, Haeckelian recapitulation, von Baer's laws, and parallelism between phylogeny and development, here formally defined as "Phylo-Devo parallelism"; and (5) Patau, Edwards, and Down syndrome (trisomies 13, 18, 21), atavisms, apoptosis, heart malformations, and medical implications. © 2015 Wiley Periodicals, Inc.

Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution.

PubMed

Orsini, Luisa; Spanier, Katina I; DE Meester, Luc

2012-05-01

Natural populations are confronted with multiple selection pressures resulting in a mosaic of environmental stressors at the landscape level. Identifying the genetic underpinning of adaptation to these complex selection environments and assigning causes of natural selection within multidimensional selection regimes in the wild is challenging. The water flea Daphnia is a renowned ecological model system with its well-documented ecology, the possibility to analyse subfossil dormant egg banks and the short generation time allowing an experimental evolution approach. Capitalizing on the strengths of this model system, we here link candidate genome regions to three selection pressures, known to induce micro-evolutionary responses in Daphnia magna: fish predation, parasitism and land use. Using a genome scan approach in space, time and experimental evolution trials, we provide solid evidence of selection at the genome level under well-characterized environmental gradients in the wild and identify candidate genes linked to the three environmental stressors. Our study reveals differential selection at the genome level in Daphnia populations and provides evidence for repeatable patterns of local adaptation in a geographic mosaic of environmental stressors fuelled by standing genetic variation. Our results imply high evolutionary potential of local populations, which is relevant to understand the dynamics of trait changes in natural populations and their impact on community and ecosystem responses through eco-evolutionary feedbacks. © 2012 Blackwell Publishing Ltd.

Mitochondria and the evolutionary roots of cancer

NASA Astrophysics Data System (ADS)

Davila, Alfonso F.; Zamorano, Pedro

2013-04-01

Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell.

Evolutionary theory of ageing and the problem of correlated Gompertz parameters.

PubMed

Burger, Oskar; Missov, Trifon I

2016-11-07

The Gompertz mortality model is often used to evaluate evolutionary theories of ageing, such as the Medawar-Williams' hypothesis that high extrinsic mortality leads to faster ageing. However, fits of the Gompertz mortality model to data often find the opposite result that mortality is negatively correlated with the rate of ageing. This negative correlation has been independently discovered in several taxa and is known in actuarial studies of ageing as the Strehler-Mildvan correlation. We examine the role of mortality selection in determining late-life variation in susceptibility to death, which has been suggested to be the cause of this negative correlation. We demonstrate that fixed-frailty models that account for heterogeneity in frailty do not remove the correlation and that the correlation is an inherent statistical property of the Gompertz distribution. Linking actuarial and biological rates of ageing will continue to be a pressing challenge, but the Strehler-Mildvan correlation itself should not be used to diagnose any biological, physiological, or evolutionary process. These findings resolve some key tensions between theory and data that affect evolutionary and biological studies of ageing and mortality. Tests of evolutionary theories of ageing should include direct measures of physiological performance or condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Feedbacks between geomorphology and biota controlling Earth surface processes and landforms: A review of foundation concepts and current understandings

NASA Astrophysics Data System (ADS)

Corenblit, Dov; Baas, Andreas C. W.; Bornette, Gudrun; Darrozes, José; Delmotte, Sébastien; Francis, Robert A.; Gurnell, Angela M.; Julien, Frédéric; Naiman, Robert J.; Steiger, Johannes

2011-06-01

This review article presents recent advances in the field of biogeomorphology related to the reciprocal coupling between Earth surface processes and landforms, and ecological and evolutionary processes. The aim is to present to the Earth Science community ecological and evolutionary concepts and associated recent conceptual developments for linking geomorphology and biota. The novelty of the proposed perspective is that (1) in the presence of geomorphologic-engineer species, which modify sediment and landform dynamics, natural selection operating at the scale of organisms may have consequences for the physical components of ecosystems, and particularly Earth surface processes and landforms; and (2) in return, these modifications of geomorphologic processes and landforms often feed back to the ecological characteristics of the ecosystem (structure and function) and thus to biological characteristics of engineer species and/or other species (adaptation and speciation). The main foundation concepts from ecology and evolutionary biology which have led only recently to an improved conception of landform dynamics in geomorphology are reviewed and discussed. The biogeomorphologic macroevolutionary insights proposed explicitly integrate geomorphologic niche-dimensions and processes within an ecosystem framework and reflect current theories of eco-evolutionary and ecological processes. Collectively, these lead to the definition of an integrated model describing the overall functioning of biogeomorphologic systems over ecological and evolutionary timescales.

Erasmus Darwin, Herbert Spencer, and the origins of the evolutionary worldview in British provincial scientific culture, 1770-1850.

PubMed

Elliott, Paul

2003-03-01

The significance of Herbert Spencer's evolutionary philosophy has been generally recognized for over a century, as the familiarity of his phrase "survival of the fittest" indicates, yet accounts of the origins of his system still tend to follow too closely his own description, written many decades later. This essay argues that Spencer's own interpretation of his intellectual development gives an inadequate impression of the debt he owed to provincial scientific culture and its institutions. Most important, it shows that his evolutionism was originally stimulated by his association with the Derby philosophical community, for it was through this group--of which his father, who also appears to have espoused a deistic evolutionary theory, was a member--that he was first exposed to progressive Englightenment social and educational philosophies and to the evolutionary worldview of Erasmus Darwin, the first president of the Derby Philosophical Society. Darwin's scheme was the first to incorporate biological evolution, associationist psychology, evolutionary geology, and cosmological developmentalism. Spencer's own implicit denials of the link with Darwin are shown to be implausible in the face of Darwin's continuing influence on the Derby savants, the product of insecurity in his later years when he feared for his reputation as Lamarckism became increasingly untenable.

Ecology and evolution of plant–pollinator interactions

PubMed Central

Mitchell, Randall J.; Irwin, Rebecca E.; Flanagan, Rebecca J.; Karron, Jeffrey D.

2009-01-01

Background Some of the most exciting advances in pollination biology have resulted from interdisciplinary research combining ecological and evolutionary perspectives. For example, these two approaches have been essential for understanding the functional ecology of floral traits, the dynamics of pollen transport, competition for pollinator services, and patterns of specialization and generalization in plant–pollinator interactions. However, as research in these and other areas has progressed, many pollination biologists have become more specialized in their research interests, focusing their attention on either evolutionary or ecological questions. We believe that the continuing vigour of a synthetic and interdisciplinary field like pollination biology depends on renewed connections between ecological and evolutionary approaches. Scope In this Viewpoint paper we highlight the application of ecological and evolutionary approaches to two themes in pollination biology: (1) links between pollinator behaviour and plant mating systems, and (2) generalization and specialization in pollination systems. We also describe how mathematical models and synthetic analyses have broadened our understanding of pollination biology, especially in human-modified landscapes. We conclude with several suggestions that we hope will stimulate future research. This Viewpoint also serves as the introduction to this Special Issue on the Ecology and Evolution of Plant–Pollinator Interactions. These papers provide inspiring examples of the synergy between evolutionary and ecological approaches, and offer glimpses of great accomplishments yet to come. PMID:19482881

Ecology and evolution of plant-pollinator interactions.

PubMed

Mitchell, Randall J; Irwin, Rebecca E; Flanagan, Rebecca J; Karron, Jeffrey D

2009-06-01

Some of the most exciting advances in pollination biology have resulted from interdisciplinary research combining ecological and evolutionary perspectives. For example, these two approaches have been essential for understanding the functional ecology of floral traits, the dynamics of pollen transport, competition for pollinator services, and patterns of specialization and generalization in plant-pollinator interactions. However, as research in these and other areas has progressed, many pollination biologists have become more specialized in their research interests, focusing their attention on either evolutionary or ecological questions. We believe that the continuing vigour of a synthetic and interdisciplinary field like pollination biology depends on renewed connections between ecological and evolutionary approaches. In this Viewpoint paper we highlight the application of ecological and evolutionary approaches to two themes in pollination biology: (1) links between pollinator behaviour and plant mating systems, and (2) generalization and specialization in pollination systems. We also describe how mathematical models and synthetic analyses have broadened our understanding of pollination biology, especially in human-modified landscapes. We conclude with several suggestions that we hope will stimulate future research. This Viewpoint also serves as the introduction to this Special Issue on the Ecology and Evolution of Plant-Pollinator Interactions. These papers provide inspiring examples of the synergy between evolutionary and ecological approaches, and offer glimpses of great accomplishments yet to come.

Individual heterogeneity in life histories and eco-evolutionary dynamics

PubMed Central

Vindenes, Yngvild; Langangen, Øystein

2015-01-01

Individual heterogeneity in life history shapes eco-evolutionary processes, and unobserved heterogeneity can affect demographic outputs characterising life history and population dynamical properties. Demographic frameworks like matrix models or integral projection models represent powerful approaches to disentangle mechanisms linking individual life histories and population-level processes. Recent developments have provided important steps towards their application to study eco-evolutionary dynamics, but so far individual heterogeneity has largely been ignored. Here, we present a general demographic framework that incorporates individual heterogeneity in a flexible way, by separating static and dynamic traits (discrete or continuous). First, we apply the framework to derive the consequences of ignoring heterogeneity for a range of widely used demographic outputs. A general conclusion is that besides the long-term growth rate lambda, all parameters can be affected. Second, we discuss how the framework can help advance current demographic models of eco-evolutionary dynamics, by incorporating individual heterogeneity. For both applications numerical examples are provided, including an empirical example for pike. For instance, we demonstrate that predicted demographic responses to climate warming can be reversed by increased heritability. We discuss how applications of this demographic framework incorporating individual heterogeneity can help answer key biological questions that require a detailed understanding of eco-evolutionary dynamics. PMID:25807980

Progress in life's history: Linking Darwinism and palaeontology in Britain, 1860-1914.

PubMed

Manias, Chris

2017-12-01

This paper examines the tension between Darwinian evolution and palaeontological research in Britain in the 1860-1914 period, looking at how three key promoters of Darwinian thinking - Thomas Henry Huxley, Edwin Ray Lankester and Alfred Russell Wallace - integrated palaeontological ideas and narratives of life's history into their public presentations of evolutionary theory. It shows how engagement with palaeontological science was an important part of the promotion of evolutionary ideas in Britain, which often bolstered notions that evolution depended upon progress and development along a wider plan. While often critical of some of the non-Darwinian concepts of evolution professed by many contemporary palaeontologists, and frequently citing the 'imperfection' of the fossil record itself, Darwinian thinkers nevertheless engaged extensively with palaeontology to develop evolutionary narratives informed by notions of improvement and progress within the natural world. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Costly Advertising and the Evolution of Cooperation

PubMed Central

Brede, Markus

2013-01-01

In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect) and a binary ‘advertising’ strategy (advertise or don’t advertise). Advertising, which comes at a cost , allows investment into faster propagation of the agents’ traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations. PMID:23861752

Costly advertising and the evolution of cooperation.

PubMed

Brede, Markus

2013-01-01

In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect) and a binary 'advertising' strategy (advertise or don't advertise). Advertising, which comes at a cost [Formula: see text], allows investment into faster propagation of the agents' traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations.

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome

PubMed Central

Naville, Magali; Ishibashi, Minaka; Ferg, Marco; Bengani, Hemant; Rinkwitz, Silke; Krecsmarik, Monika; Hawkins, Thomas A.; Wilson, Stephen W.; Manning, Elizabeth; Chilamakuri, Chandra S. R.; Wilson, David I.; Louis, Alexandra; Lucy Raymond, F.; Rastegar, Sepand; Strähle, Uwe; Lenhard, Boris; Bally-Cuif, Laure; van Heyningen, Veronica; FitzPatrick, David R.; Becker, Thomas S.; Roest Crollius, Hugues

2015-01-01

Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression. PMID:25908307

Recent advances in the evolutionary engineering of industrial biocatalysts.

PubMed

Winkler, James D; Kao, Katy C

2014-12-01

Evolutionary engineering has been used to improve key industrial strain traits, such as carbon source utilization, tolerance to adverse environmental conditions, and resistance to chemical inhibitors, for many decades due to its technical simplicity and effectiveness. The lack of need for prior genetic knowledge underlying the phenotypes of interest makes this a powerful approach for strain development for even species with minimal genotypic information. While the basic experimental procedure for laboratory adaptive evolution has remained broadly similar for many years, a range of recent advances show promise for improving the experimental workflows for evolutionary engineering by accelerating the pace of evolution, simplifying the analysis of evolved mutants, and providing new ways of linking desirable phenotypes to selectable characteristics. This review aims to highlight some of these recent advances and discuss how they may be used to improve industrially relevant microbial phenotypes. Copyright © 2014 Elsevier Inc. All rights reserved.

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.

PubMed

Clifton, Ben E; Kaczmarski, Joe A; Carr, Paul D; Gerth, Monica L; Tokuriki, Nobuhiko; Jackson, Colin J

2018-04-23

The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.

The gastrointestinal-brain axis in humans as an evolutionary advance of the root-leaf axis in plants: A hypothesis linking quantum effects of light on serotonin and auxin.

PubMed

Tonello, Lucio; Gashi, Bekim; Scuotto, Alessandro; Cappello, Glenda; Cocchi, Massimo; Gabrielli, Fabio; Tuszynski, Jack A

2018-01-01

Living organisms tend to find viable strategies under ambient conditions that optimize their search for, and utilization of, life-sustaining resources. For plants, a leading role in this process is performed by auxin, a plant hormone that drives morphological development, dynamics, and movement to optimize the absorption of light (through branches and leaves) and chemical "food" (through roots). Similarly to auxin in plants, serotonin seems to play an important role in higher animals, especially humans. Here, it is proposed that morphological and functional similarities between (i) plant leaves and the animal/human brain and (ii) plant roots and the animal/human gastro-intestinal tract have general features in common. Plants interact with light and use it for biological energy, whereas, neurons in the central nervous system seem to interact with bio-photons and use them for proper brain function. Further, as auxin drives roots "arborescence" within the soil, similarly serotonin seems to facilitate enteric nervous system connectivity within the human gastro-intestinal tract. This auxin/serotonin parallel suggests the root-branches axis in plants may be an evolutionary precursor to the gastro-intestinal-brain axis in humans. Finally, we hypothesize that light might be an important factor, both in gastro-intestinal dynamics and brain function. Such a comparison may indicate a key role for the interaction of light and serotonin in neuronal physiology (possibly in both the central nervous system and the enteric nervous system), and according to recent work, mind and consciousness.

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.

PubMed

Naval-Sanchez, Marina; Nguyen, Quan; McWilliam, Sean; Porto-Neto, Laercio R; Tellam, Ross; Vuocolo, Tony; Reverter, Antonio; Perez-Enciso, Miguel; Brauning, Rudiger; Clarke, Shannon; McCulloch, Alan; Zamani, Wahid; Naderi, Saeid; Rezaei, Hamid Reza; Pompanon, Francois; Taberlet, Pierre; Worley, Kim C; Gibbs, Richard A; Muzny, Donna M; Jhangiani, Shalini N; Cockett, Noelle; Daetwyler, Hans; Kijas, James

2018-02-28

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.

Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

PubMed

O'Malley, Maureen A

2012-01-01

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia

PubMed Central

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M.

2016-01-01

Abstract Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints. PMID:28175287

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.

PubMed

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M; Ruiz-Herrera, Aurora

2016-12-01

Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.

Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains

PubMed Central

Cotton, Allison M.; Chen, Chih-Yu; Lam, Lucia L.; Wasserman, Wyeth W.; Kobor, Michael S.; Brown, Carolyn J.

2014-01-01

X-chromosome inactivation results in dosage equivalence between the X chromosome in males and females; however, over 15% of human X-linked genes escape silencing and these genes are enriched on the evolutionarily younger short arm of the X chromosome. The spread of inactivation onto translocated autosomal material allows the study of inactivation without the confounding evolutionary history of the X chromosome. The heterogeneity and reduced extent of silencing on autosomes are evidence for the importance of DNA elements underlying the spread of silencing. We have assessed DNA methylation in six unbalanced X-autosome translocations using the Illumina Infinium HumanMethylation450 array. Two to 42% of translocated autosomal genes showed this mark of silencing, with the highest degree of inactivation observed for trisomic autosomal regions. Generally, the extent of silencing was greatest close to the translocation breakpoint; however, silencing was detected well over 100 kb into the autosomal DNA. Alu elements were found to be enriched at autosomal genes that escaped from inactivation while L1s were enriched at subject genes. In cells without the translocation, there was enrichment of heterochromatic features such as EZH2 and H3K27me3 for those genes that become silenced when translocated, suggesting that underlying chromatin structure predisposes genes towards silencing. Additionally, the analysis of topological domains indicated physical clustering of autosomal genes of common inactivation status. Overall, our analysis indicated a complex interaction between DNA sequence, chromatin features and the three-dimensional structure of the chromosome. PMID:24158853

Maximizing ecological and evolutionary insight in bisulfite sequencing data sets

PubMed Central

Lea, Amanda J.; Vilgalys, Tauras P.; Durst, Paul A.P.; Tung, Jenny

2017-01-01

Preface Genome-scale bisulfite sequencing approaches have opened the door to ecological and evolutionary studies of DNA methylation in many organisms. These approaches can be powerful. However, they introduce new methodological and statistical considerations, some of which are particularly relevant to non-model systems. Here, we highlight how these considerations influence a study’s power to link methylation variation with a predictor variable of interest. Relative to current practice, we argue that sample sizes will need to increase to provide robust insights. We also provide recommendations for overcoming common challenges and an R Shiny app to aid in study design. PMID:29046582

Differences in the selection response of serially repeated color pattern characters: standing variation, development, and evolution.

PubMed

Allen, Cerisse E; Beldade, Patrícia; Zwaan, Bas J; Brakefield, Paul M

2008-03-26

There is spectacular morphological diversity in nature but lineages typically display a limited range of phenotypes. Because developmental processes generate the phenotypic variation that fuels natural selection, they are a likely source of evolutionary biases, facilitating some changes and limiting others. Although shifts in developmental regulation are associated with morphological differences between taxa, it is unclear how underlying mechanisms affect the rate and direction of evolutionary change within populations under selection. Here we focus on two ecologically relevant features of butterfly wing color patterns, eyespot size and color composition, which are similarly and strongly correlated across the serially repeated eyespots. Though these two characters show similar patterns of standing variation and covariation within a population, they differ in key features of their underlying development. We targeted pairs of eyespots with artificial selection for coordinated (concerted selection) versus independent (antagonistic selection) change in their color composition and size and compared evolutionary responses of the two color pattern characters. The two characters respond to selection in strikingly different ways despite initially similar patterns of variation in all directions present in the starting population. Size (determined by local properties of a diffusing inductive signal) evolves flexibly in all selected directions. However, color composition (determined by a tissue-level response to the signal concentration gradient) evolves only in the direction of coordinated change. There was no independent evolutionary change in the color composition of two eyespots in response to antagonistic selection. Moreover, these differences in the directions of short-term evolutionary change in eyespot size and color composition within a single species are consistent with the observed wing pattern diversity in the genus. Both characters respond rapidly to selection for coordinated change, but there are striking differences in their response to selection for antagonistic, independent change across eyespots. While many additional factors may contribute to both short- and long-term evolutionary response, we argue that the compartmentalization of developmental processes can influence the diversification of serial repeats such as butterfly eyespots, even under strong selection.

iPHLoc-ES: Identification of bacteriophage protein locations using evolutionary and structural features.

PubMed

Shatabda, Swakkhar; Saha, Sanjay; Sharma, Alok; Dehzangi, Abdollah

2017-12-21

Bacteriophage proteins are viruses that can significantly impact on the functioning of bacteria and can be used in phage based therapy. The functioning of Bacteriophage in the host bacteria depends on its location in those host cells. It is very important to know the subcellular location of the phage proteins in a host cell in order to understand their working mechanism. In this paper, we propose iPHLoc-ES, a prediction method for subcellular localization of bacteriophage proteins. We aim to solve two problems: discriminating between host located and non-host located phage proteins and discriminating between the locations of host located protein in a host cell (membrane or cytoplasm). To do this, we extract sets of evolutionary and structural features of phage protein and employ Support Vector Machine (SVM) as our classifier. We also use recursive feature elimination (RFE) to reduce the number of features for effective prediction. On standard dataset using standard evaluation criteria, our method significantly outperforms the state-of-the-art predictor. iPHLoc-ES is readily available to use as a standalone tool from: https://github.com/swakkhar/iPHLoc-ES/ and as a web application from: http://brl.uiu.ac.bd/iPHLoc-ES/. Copyright © 2017 Elsevier Ltd. All rights reserved.

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family.

PubMed

Garcia, Sònia; Panero, José L; Siroky, Jiri; Kovarik, Ales

2010-08-16

In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in approximately 200 species representing the family diversity and other closely related groups. Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae.

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

PubMed Central

2010-01-01

Background In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups. Results Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Conclusions Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae. PMID:20712858

The Nuclear Receptor Rev-erbα Controls Circadian Thermogenic Plasticity

PubMed Central

Gerhart-Hines, Zachary; Everett, Logan J.; Loro, Emanuele; Briggs, Erika R.; Bugge, Anne; Hou, Catherine; Ferrara, Christine; Seale, Patrick; Pryma, Daniel A.; Khurana, Tejvir S.; Lazar, Mitchell A.

2013-01-01

Circadian oscillation of body temperature is a basic, evolutionary-conserved feature of mammalian biology1. Additionally, homeostatic pathways allow organisms to protect their core temperatures in response to cold exposure2. However, the mechanism responsible for coordinating daily body temperature rhythm and adaptability to environmental challenges is unknown. Here we show that the nuclear receptor Rev-erbα, a powerful transcriptional repressor, links circadian and thermogenic networks through the regulation of brown adipose tissue (BAT) function. Mice exposed to cold fare dramatically better at 5 AM (Zeitgeber time 22) when Rev-erbα is barely expressed than at 5 PM (ZT10) when Rev-erbα is abundant. Deletion of Rev-erbα markedly improves cold tolerance at 5 PM, indicating that overcoming Rev-erbα-dependent repression is a fundamental feature of the thermogenic response to cold. Physiological induction of uncoupling protein 1 (UCP1) by cold temperatures is preceded by rapid down-regulation of Rev-erbα in BAT. Rev-erbα represses UCP1 in a brown adipose cell-autonomous manner and BAT UCP1 levels are high in Rev-erbα-null mice even at thermoneutrality. Genetic loss of Rev-erbα also abolishes normal rhythms of body temperature and BAT activity. Thus, Rev-erbα acts as a thermogenic focal point required for establishing and maintaining body temperature rhythm in a manner that is adaptable to environmental demands. PMID:24162845

How the environment shapes animal signals: a test of the acoustic adaptation hypothesis in frogs.

PubMed

Goutte, S; Dubois, A; Howard, S D; Márquez, R; Rowley, J J L; Dehling, J M; Grandcolas, P; Xiong, R C; Legendre, F

2018-01-01

Long-distance acoustic signals are widely used in animal communication systems and, in many cases, are essential for reproduction. The acoustic adaptation hypothesis (AAH) implies that acoustic signals should be selected for further transmission and better content integrity under the acoustic constraints of the habitat in which they are produced. In this study, we test predictions derived from the AAH in frogs. Specifically, we focus on the difference between torrent frogs and frogs calling in less noisy habitats. Torrents produce sounds that can mask frog vocalizations and constitute a major acoustic constraint on call evolution. We combine data collected in the field, material from scientific collections and the literature for a total of 79 primarily Asian species, of the families Ranidae, Rhacophoridae, Dicroglossidae and Microhylidae. Using phylogenetic comparative methods and including morphological and environmental potential confounding factors, we investigate putatively adaptive call features in torrent frogs. We use broad habitat categories as well as fine-scale habitat measurements and test their correlation with six call characteristics. We find mixed support for the AAH. Spectral features of torrent frog calls are different from those of frogs calling in other habitats and are related to ambient noise levels, as predicted by the AAH. However, temporal call features do not seem to be shaped by the frogs' calling habitats. Our results underline both the complexity of call evolution and the need to consider multiple factors when investigating this issue. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Mirror writing ability is genetic and probably transmitted as a sex-linked dominant trait: it is hypothesised that mirror writers have bilateral language centres with a callosal interconnection.

PubMed

Mathewson, Iain

2004-01-01

Mirror writing is the ability to write from right to left, reversing each letter so that when held to a mirror the script appears normal. There is no information on the prevalence of this trait but a suggestion was received that it may be hereditary. A newspaper survey was carried out to discover the approximate prevalence and whether a hereditary factor is involved. The results indicated a prevalence of 1 in 6500. There is strong evidence that the trait is hereditary and is associated with non-right-handedness'. It is hypothesised that mirror writers may comprise a very small group of people who not only have bilateral language centres but also have an interconnecting pathway between these centres via the corpus callosum. The surprising genetic nature of a trait with no obvious evolutionary consequences is discussed. The data can best be explained on the basis of the trait being the phenotypic expression of an X-linked dominant gene, which does have evolutionary consequences. Similarities are noted between the proposed genetics of mirror writing and those of synaesthesia and of a few pathological X-linked dominant syndromes such as Rett syndrome. Other similarities and contrasts between mirror writing and synaesthesia are noted.

EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms.

PubMed

Rapakoulia, Trisevgeni; Theofilatos, Konstantinos; Kleftogiannis, Dimitrios; Likothanasis, Spiros; Tsakalidis, Athanasios; Mavroudi, Seferina

2014-08-15

Single nucleotide polymorphisms (SNPs) are considered the most frequently occurring DNA sequence variations. Several computational methods have been proposed for the classification of missense SNPs to neutral and disease associated. However, existing computational approaches fail to select relevant features by choosing them arbitrarily without sufficient documentation. Moreover, they are limited to the problem of missing values, imbalance between the learning datasets and most of them do not support their predictions with confidence scores. To overcome these limitations, a novel ensemble computational methodology is proposed. EnsembleGASVR facilitates a two-step algorithm, which in its first step applies a novel evolutionary embedded algorithm to locate close to optimal Support Vector Regression models. In its second step, these models are combined to extract a universal predictor, which is less prone to overfitting issues, systematizes the rebalancing of the learning sets and uses an internal approach for solving the missing values problem without loss of information. Confidence scores support all the predictions and the model becomes tunable by modifying the classification thresholds. An extensive study was performed for collecting the most relevant features for the problem of classifying SNPs, and a superset of 88 features was constructed. Experimental results show that the proposed framework outperforms well-known algorithms in terms of classification performance in the examined datasets. Finally, the proposed algorithmic framework was able to uncover the significant role of certain features such as the solvent accessibility feature, and the top-scored predictions were further validated by linking them with disease phenotypes. Datasets and codes are freely available on the Web at http://prlab.ceid.upatras.gr/EnsembleGASVR/dataset-codes.zip. All the required information about the article is available through http://prlab.ceid.upatras.gr/EnsembleGASVR/site.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Early Adversity, Elevated Stress Physiology, Accelerated Sexual Maturation, and Poor Health in Females

ERIC Educational Resources Information Center

Belsky, Jay; Ruttle, Paula L.; Boyce, W. Thomas; Armstrong, Jeffrey M.; Essex, Marilyn J.

2015-01-01

Evolutionary-minded developmentalists studying predictive-adaptive-response processes linking childhood adversity with accelerated female reproductive development and health scientists investigating the developmental origins of health and disease (DOoHaD) may be tapping the same process, whereby longer-term health costs are traded off for…

Honey Bee Aggression Supports a Link Between Gene Regulation and Behavioral Evolution

USDA-ARS?s Scientific Manuscript database

A prominent theory holds that animal phenotypes arise by evolutionary changes in the regulation of gene expression. Emerging from studies of animal development, evidence for this theory consists largely of differences in temporal or spatial patterns of gene expression that are related to morphologi...

Mitochondrial Fitness, Gene Expression, and Hypoxic Stress in a Hybrid Population of the Killifish, Fundulus Heteroclitus

EPA Science Inventory

The physiological link between oxygen availability and mitochondrial function is well established. However, whether or not fitness variation is associated with mitochondrial genotypes in the field remains a contested topic in evolutionary biology. In this study we draw on a popul...

Linking environmental flows to sediment dynamics

Treesearch

Diego García de Jalón; Martina Bussettini; Massimo Rinaldi; Gordon Grant; Nikolai Friberg; Ian G. Cowx; Fernando Magdaleno; Tom Buijse

2016-01-01

This is a policy discussion paper aimed at addressing possible alternative approaches for environmental flows (e-Flows) assessment and identification within the context of best strategies for fluvial restoration. We focus on dammed rivers in Mediterranean regions. Fluvial species and their ecological integrity are the result of their evolutionary adaptation to river...

Multinational Corporations, Democracy and Child Mortality: A Quantitative, Cross-National Analysis of Developing Countries

ERIC Educational Resources Information Center

Shandra, John M.; Nobles, Jenna E.; London, Bruce; Williamson, John B.

2005-01-01

This study presents quantitative, sociological models designed to account for cross-national variation in child mortality. We consider variables linked to five different theoretical perspectives that include the economic modernization, social modernization, political modernization, ecological-evolutionary, and dependency perspectives. The study is…

The Role of Nuclear Receptor Coactivators in Recurrent Prostate Cancer

DTIC Science & Technology

2006-02-01

hyp- oplasia congenita and hypogonadotropic hypogonadism (34). From an evolutionary perspective, the AR AF2 region of the ligand binding domain is more...linked adrenal hypoplasia congenita and hypogo- nadotropic hypogonadism . Nature 372:672–676. 35. Muscatelli, F., A. P. Walker, E. De Plaen, A. N

Hypotheses generation as supervised link discovery with automated class labeling on large-scale biomedical concept networks

PubMed Central

2012-01-01

Computational approaches to generate hypotheses from biomedical literature have been studied intensively in recent years. Nevertheless, it still remains a challenge to automatically discover novel, cross-silo biomedical hypotheses from large-scale literature repositories. In order to address this challenge, we first model a biomedical literature repository as a comprehensive network of biomedical concepts and formulate hypotheses generation as a process of link discovery on the concept network. We extract the relevant information from the biomedical literature corpus and generate a concept network and concept-author map on a cluster using Map-Reduce frame-work. We extract a set of heterogeneous features such as random walk based features, neighborhood features and common author features. The potential number of links to consider for the possibility of link discovery is large in our concept network and to address the scalability problem, the features from a concept network are extracted using a cluster with Map-Reduce framework. We further model link discovery as a classification problem carried out on a training data set automatically extracted from two network snapshots taken in two consecutive time duration. A set of heterogeneous features, which cover both topological and semantic features derived from the concept network, have been studied with respect to their impacts on the accuracy of the proposed supervised link discovery process. A case study of hypotheses generation based on the proposed method has been presented in the paper. PMID:22759614

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

PubMed

Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

2002-08-01

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis

PubMed Central

Chu, Xin-Yi; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-01-01

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information. PMID:28708071

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis.

PubMed

Chu, Xin-Yi; Jiang, Ling-Han; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-07-14

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.

Evolutionary synthesis of simple stellar populations. Colours and indices

NASA Astrophysics Data System (ADS)

Kurth, O. M.; Fritze-v. Alvensleben, U.; Fricke, K. J.

1999-07-01

We construct evolutionary synthesis models for simple stellar populations using the evolutionary tracks from the Padova group (1993, 1994), theoretical colour calibrations from \\cite[Lejeune et al. (1997, 1998)]{lejeune} and fit functions for stellar atmospheric indices from \\cite[Worthey et al. (1994)]{worthey}. A Monte-Carlo technique allows us to obtain a smooth time evolution of both broad band colours in UBVRIK and a series of stellar absorption features for Single Burst Stellar Populations (SSPs). We present colours and indices for SSPs with ages from 1 \\ 10(9) yrs to 1.6 \\ 10(10) yrs and metallicities [M/H]=-2.3, -1.7, -0.7, -0.4, 0.0 and 0.4. Model colours and indices at an age of about a Hubble time are in good agreement with observed colours and indices of the Galactic and M 31 GCs.

Evolutionary trends in arvicolids and the endemic murid Mikrotia - New data and a critical overview

NASA Astrophysics Data System (ADS)

Maul, Lutz C.; Masini, Federico; Parfitt, Simon A.; Rekovets, Leonid; Savorelli, Andrea

2014-07-01

The study of evolutionary rates dates back to the work of Simpson and Haldane in the 1940s. Small mammals, especially Plio-Pleistocene arvicolids (voles and lemmings), are particularly suited for such studies because they have an unusually complete fossil record and exhibit significant evolutionary change through time. In recent decades, arvicolids have been the focus of intensive research devoted to the tempo and mode of evolutionary change and the identification of trends in dental evolution that can be used to correlate and date fossil sites. These studies have raised interesting questions about whether voles and lemmings had unique evolutionary trajectories, or show convergent evolutionary patterns with other hypsodont rodents. Here we review evolutionary patterns in selected arvicolid lineages and endemic Messinian murids (Mikrotia spp.) and discuss reasons for convergence in dental morphology in these two groups of hypsodont rodents. The results substantiate previously detected patterns, but the larger dataset shows that some trends are less regular than previous studies have suggested. With the exception of a pervasive and sustained trend towards increased hypsodonty, our results show that other features do not follow consistent patterns in all lineages, exhibiting a mosaic pattern comprising stasis, variable rate evolution and gradual unidirectional change through time. Evidence for higher evolutionary rates is found in lineages apparently undergoing adaptations to new ecological niches. In the case of Mikrotia, Microtus voles and the water vole (Mimomys-Arvicola) lineage, a shift to a fossorial lifestyle appears to have been an important driving force in their evolution. For other characters, different causes can be invoked; for example a shift to a semi-aquatic lifestyle may be responsible for the trend towards increasing size in Arvicola. Biochronological application of the data should take into account the complexity and biases of the data.

Identification and characterization of integrin-binding sialoprotein (IBSP) genes in reptile and amphibian.

PubMed

Shintani, Seikou; Kamakura, Naofumi; Kobata, Mitsuhiko; Toyosawa, Satoru; Onishi, Tomoyuki; Sato, Akie; Kawasaki, Kazuhiko; Weiss, Kenneth M; Ooshima, Takashi

2008-11-15

Integrin-binding sialoprotein (IBSP) is a member of the small integrin-binding ligand N-linked glycoprotein (SIBLING) family; and the whole SIBLING family is further included in a larger secretory calcium-binding phosphoprotein (SCPP) family. SIBLING proteins are known to construct a part of the non-collagenous extracellular matrices of calcified tissues, and considered to have arisen by duplication and subsequent divergent evolution of a single ancient gene. To understand the alterations of SIBLING molecules associated with the evolution of calcified tissues in vertebrates, we initiated a search for lower vertebrate orthologs of SIBLING genes. In the present study, an IBSP ortholog from a reptile (caiman) and two distinct orthologs from an amphibian (African clawed toad) were identified and characterized. As expected, the toad IBSP genes were transcribed only in calcified tissue (jaw and tibia), as also seen in mammals. The caiman, toad, avian, and mammalian IBSPs share several unique features specific for IBSP and apparently have similar properties. Furthermore, analysis of the sequences suggested that the IBSP molecule might have gradually intensified its functions related to calcification during its evolutionary process through tetrapods.

Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels.

PubMed

Lomash, Suvendu; Chittori, Sagar; Brown, Patrick; Mayer, Mark L

2013-03-05

AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine, and phenylalanine, which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate, and serine. AvGluR1 LBD crystal structures reveal an unusual scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, whereas in the alanine, methionine, and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl(-) lowers affinity for these ligands but not for glutamate or aspartate nor for phenylalanine, which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure-based studies on iGluR-ligand interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors

PubMed Central

Qin, Xin-Cheng; Shi, Mang; Tian, Jun-Hua; Lin, Xian-Dan; Gao, Dong-Ya; He, Jin-Rong; Wang, Jian-Bo; Li, Ci-Xiu; Kang, Yan-Jun; Yu, Bin; Zhou, Dun-Jin; Xu, Jianguo; Plyusnin, Alexander; Holmes, Edward C.; Zhang, Yong-Zhen

2014-01-01

Although segmented and unsegmented RNA viruses are commonplace, the evolutionary links between these two very different forms of genome organization are unclear. We report the discovery and characterization of a tick-borne virus—Jingmen tick virus (JMTV)—that reveals an unexpected connection between segmented and unsegmented RNA viruses. The JMTV genome comprises four segments, two of which are related to the nonstructural protein genes of the genus Flavivirus (family Flaviviridae), whereas the remaining segments are unique to this virus, have no known homologs, and contain a number of features indicative of structural protein genes. Remarkably, homology searching revealed that sequences related to JMTV were present in the cDNA library from Toxocara canis (dog roundworm; Nematoda), and that shared strong sequence and structural resemblances. Epidemiological studies showed that JMTV is distributed in tick populations across China, especially Rhipicephalus and Haemaphysalis spp., and experiences frequent host-switching and genomic reassortment. To our knowledge, JMTV is the first example of a segmented RNA virus with a genome derived in part from unsegmented viral ancestors. PMID:24753611

Improved Evolutionary Hybrids for Flexible Ligand Docking in Autodock

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belew, R.K.; Hart, W.E.; Morris, G.M.

1999-01-27

In this paper we evaluate the design of the hybrid evolutionary algorithms (EAs) that are currently used to perform flexible ligand binding in the Autodock docking software. Hybrid EAs incorporate specialized operators that exploit domain-specific features to accelerate an EA's search. We consider hybrid EAs that use an integrated local search operator to reline individuals within each iteration of the search. We evaluate several factors that impact the efficacy of a hybrid EA, and we propose new hybrid EAs that provide more robust convergence to low-energy docking configurations than the methods currently available in Autodock.

Parallel evolution of image processing tools for multispectral imagery

NASA Astrophysics Data System (ADS)

Harvey, Neal R.; Brumby, Steven P.; Perkins, Simon J.; Porter, Reid B.; Theiler, James P.; Young, Aaron C.; Szymanski, John J.; Bloch, Jeffrey J.

2000-11-01

We describe the implementation and performance of a parallel, hybrid evolutionary-algorithm-based system, which optimizes image processing tools for feature-finding tasks in multi-spectral imagery (MSI) data sets. Our system uses an integrated spatio-spectral approach and is capable of combining suitably-registered data from different sensors. We investigate the speed-up obtained by parallelization of the evolutionary process via multiple processors (a workstation cluster) and develop a model for prediction of run-times for different numbers of processors. We demonstrate our system on Landsat Thematic Mapper MSI , covering the recent Cerro Grande fire at Los Alamos, NM, USA.

Sex-Linked Behavior: Evolution, Stability, and Variability.

PubMed

Fine, Cordelia; Dupré, John; Joel, Daphna

2017-07-29

Common understanding of human sex-linked behaviors is that proximal mechanisms of genetic and hormonal sex, ultimately shaped by the differential reproductive challenges of ancestral males and females, act on the brain to transfer sex-linked predispositions across generations. Here, we extend the debate on the role of nature and nurture in the development of traits in the lifetime of an individual, to their role in the cross-generation transfer of traits. Advances in evolutionary theory that posit the environment as a source of trans-generational stability, and new understanding of sex effects on the brain, suggest that the cross-generation stability of sex-linked patterns of behavior are sometimes better explained in terms of inherited socioenvironmental conditions, with biological sex fostering intrageneration variability. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sex-Linked Behavior: Evolution, Stability, and Variability.

PubMed

Fine, Cordelia; Dupré, John; Joel, Daphna

2017-09-01

Common understanding of human sex-linked behaviors is that proximal mechanisms of genetic and hormonal sex, ultimately shaped by the differential reproductive challenges of ancestral males and females, act on the brain to transfer sex-linked predispositions across generations. Here, we extend the debate on the role of nature and nurture in the development of traits in the lifetime of an individual, to their role in the cross-generation transfer of traits. Advances in evolutionary theory that posit the environment as a source of trans-generational stability, and new understanding of sex effects on the brain, suggest that the cross-generation stability of sex-linked patterns of behavior are sometimes better explained in terms of inherited socioenvironmental conditions, with biological sex fostering intrageneration variability. Copyright © 2017 Elsevier Ltd. All rights reserved.

Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories

PubMed Central

Liu, Yang; El-Kassaby, Yousry A.

2017-01-01

While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18–24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration. We applied diverse profiling methods to examine sRNA and miRNA features, including size distribution, sequence conservation and reproduction-specific regulation, as well as to predict their putative targets. The top 27 most abundant miRNAs were highly overlapped between the two species (e.g., miR166,−319 and−396), but in P. glauca, they were less abundant and significantly less correlated with seed-set phases. The most abundant sRNAs in libraries were deeply conserved miRNAs in the plant kingdom for Arabidopsis but long sRNAs (24-nt) for P. glauca. We also found significant difference in normalized expression between populations for population-specific sRNAs but not for lineage-specific ones. Moreover, lineage-specific sRNAs were enriched in the 21-nt size class. This pattern is consistent in both species and alludes to a specific type of sRNAs (e.g., miRNA, tasiRNA) being selected for. In addition, we deemed 24 and 9 sRNAs in P. glauca and Arabidopsis, respectively, as sRNA candidates targeting known adaptive genes. Temperature had significant influence on selected gene and miRNA expression at seed development in both species. This study increases our integrated understanding of sRNA evolution and its potential link to genomic architecture (e.g., sRNA derivation from genome and sRNA-mediated genomic events) and organismal complexity (e.g., association between different sRNA expression and their functionality). PMID:29046688

Predicting links based on knowledge dissemination in complex network

NASA Astrophysics Data System (ADS)

Zhou, Wen; Jia, Yifan

2017-04-01

Link prediction is the task of mining the missing links in networks or predicting the next vertex pair to be connected by a link. A lot of link prediction methods were inspired by evolutionary processes of networks. In this paper, a new mechanism for the formation of complex networks called knowledge dissemination (KD) is proposed with the assumption of knowledge disseminating through the paths of a network. Accordingly, a new link prediction method-knowledge dissemination based link prediction (KDLP)-is proposed to test KD. KDLP characterizes vertex similarity based on knowledge quantity (KQ) which measures the importance of a vertex through H-index. Extensive numerical simulations on six real-world networks demonstrate that KDLP is a strong link prediction method which performs at a higher prediction accuracy than four well-known similarity measures including common neighbors, local path index, average commute time and matrix forest index. Furthermore, based on the common conclusion that an excellent link prediction method reveals a good evolving mechanism, the experiment results suggest that KD is a considerable network evolving mechanism for the formation of complex networks.

Aeolian Rat Tails (ARTs): A New Morphological Indicator of Abrasion Direction

NASA Astrophysics Data System (ADS)

Favaro, E. A.; Hugenholtz, C.; Barchyn, T.

2016-12-01

Aeolian rat tails (ARTs) are a previously undocumented aeolian abrasion feature observed on ignimbrite surfaces in the Puna Plateau of Northwest Argentina and bare morphological similarity to small-scale features on Mars. We describe the terrestrial features and present an evolutionary sequence from inception to demise. ARTs are regionally-ubiquitous and characterized by a windward abrasion-resistant lithic clast and a downwind-tapering tail. The size of ARTs is controlled by the diameter of the windward lithic clast, observed on the sub-decimeter to meter scale. Their distribution throughout the Campo de Piedra Pómez, and adjacent regions is determined by the ignimbrite clast content. ARTs develop under a uni-modal abrasion direction when lithic clasts are eroded out of the ignimbrite matrix, protrude from the surface, and shelter material directly behind the clast. As the surrounding material is eroded away, a downwind-tapered tail develops. Continued erosion of the adjacent surface leads to the undercutting of clasts, liberating them from the feature where, if small enough, the clasts can be transported downwind, leading to the destruction of the tail and ultimately the feature. This evolutionary sequence accounts not only for the morphology of the feature, but also the presence of loose clasts on the ignimbrite surface, which plays a role in the development of other enigmatic landforms in the area, such as periodic bedrock ridges, yardangs, and megaripples. The significance of the identification of ARTs is due to the necessity of uni-modal abrasion direction for their development, thereby making their orientation a diagnostic indicator of long-term aeolian abrasion direction. ARTs are likely analogs of features identified by MSL Curiosity Rover on Mars, possibly providing information on past and present wind regimes.

Pathways to cognitive design.

PubMed

Wertz, Annie E; Moya, Cristina

2018-05-30

Despite a shared recognition that the design of the human mind and the design of human culture are tightly linked, researchers in the evolutionary social sciences tend to specialize in understanding one at the expense of the other. The disciplinary boundaries roughly correspond to research traditions that focus more on natural selection and those that focus more on cultural evolution. In this paper, we articulate how two research traditions within the evolutionary social sciences-evolutionary psychology and cultural evolution-approach the study of design. We focus our analysis on the design of cognitive mechanisms that are the result of the interplay of genetic and cultural evolution. We aim to show how the approaches of these two research traditions can complement each other, and provide a framework for developing a wider range of testable hypotheses about cognitive design. To do so, we provide concrete illustrations of how this integrated approach can be used to interrogate cognitive design using examples from our own work on plant and symbolic group boundary cognition. We hope this recognition of different pathways to design will broaden the hypothesis space in the evolutionary social sciences and encourage methodological pluralism in the investigation of the mind. Copyright © 2018 Elsevier B.V. All rights reserved.

Evolution of egg coats: linking molecular biology and ecology.

PubMed

Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

2015-08-01

One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

Evolutionary medicine.

PubMed

Swynghedauw, B

2004-04-01

Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

Evolution of the β-adrenoreceptors in vertebrates.

PubMed

Zavala, Kattina; Vandewege, Michael W; Hoffmann, Federico G; Opazo, Juan C

2017-01-01

The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information. Our results show that in addition to the three already described vertebrate β-adrenoreceptor genes there is an additional group containing cyclostome sequences. We suggest that β-adrenoreceptors diversified as a product of the two whole genome duplications that occurred in the ancestor of vertebrates. Gene expression patterns are in general consistent across species, suggesting that expression dynamics were established early in the evolutionary history of vertebrates, and have been maintained since then. Finally, amino acid polymorphisms that are associated to pathological conditions in humans appear to be common in non-human mammals, suggesting that the phenotypic effects of these mutations depend on epistatic interaction with other positions. The evolutionary analysis of the β-adrenoreceptors delivers new insights about the diversity of these receptors in vertebrates, the evolution of the expression patterns and a comparative perspective regarding the polymorphisms that in humans are linked to pathological conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

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Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

PubMed

Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

2018-04-01

Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05-79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep's recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

PubMed Central

Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

2018-01-01

Abstract Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome. PMID:29790980

Ferns are less dependent on passive dilution by cell expansion to coordinate leaf vein and stomatal spacing than angiosperms

PubMed Central

Jordan, Gregory J.; Brodribb, Timothy J.

2017-01-01

Producing leaves with closely spaced veins is a key innovation linked to high rates of photosynthesis in angiosperms. A close geometric link between veins and stomata in angiosperms ensures that investment in enhanced venous water transport provides the strongest net carbon return to the plant. This link is underpinned by “passive dilution” via expansion of surrounding cells. However, it is not known whether this ‘passive dilution’ mechanism is present in plant lineages other than angiosperms and is another key feature of the angiosperms’ evolutionary success. Consequently, we sought to determine whether the ‘passive dilution’ mechanism is; (i) exclusive to the angiosperms, (ii) a conserved mechanism that evolved in the common ancestor of ferns and angiosperms, or (iii) has evolved continuously over time. To do this we first we assessed the plasticity of vein and stomatal density and epidermal cell size in ferns in response to light environment. We then compared the relationships between these traits found among ferns with modelled relationships that assume vein and stomatal density respond passively to epidermal cell expansion, and with those previously observed in angiosperms. Vein density, stomatal density and epidermal cell size were linked in ferns with remarkably similar relationships to those observed in angiosperms, except that fern leaves had fewer veins per stomata. However, plasticity was limited in ferns and stomatal spacing was dependent on active stomatal differentiation as well as passive cell expansion. Thus, ferns (like angiosperms) appear to coordinate vein and stomatal density with epidermal cell expansion to some extent to maintain a constant ratio between veins and stomata in the leaf. The different general relationships between vein density and stomatal density in ferns and angiosperms suggests the groups have different optimum balances between the production of vein tissue dedicated to water supply and stomatal tissue for gas exchange. PMID:28953931

PrAS: Prediction of amidation sites using multiple feature extraction.

PubMed

Wang, Tong; Zheng, Wei; Wuyun, Qiqige; Wu, Zhenfeng; Ruan, Jishou; Hu, Gang; Gao, Jianzhao

2017-02-01

Amidation plays an important role in a variety of pathological processes and serious diseases like neural dysfunction and hypertension. However, identification of protein amidation sites through traditional experimental methods is time consuming and expensive. In this paper, we proposed a novel predictor for Prediction of Amidation Sites (PrAS), which is the first software package for academic users. The method incorporated four representative feature types, which are position-based features, physicochemical and biochemical properties features, predicted structure-based features and evolutionary information features. A novel feature selection method, positive contribution feature selection was proposed to optimize features. PrAS achieved AUC of 0.96, accuracy of 92.1%, sensitivity of 81.2%, specificity of 94.9% and MCC of 0.76 on the independent test set. PrAS is freely available at https://sourceforge.net/p/praspkg. Copyright © 2016 Elsevier Ltd. All rights reserved.

δ-Conotoxin SuVIA suggests an evolutionary link between ancestral predator defence and the origin of fish-hunting behaviour in carnivorous cone snails

PubMed Central

Jin, Ai-Hua; Israel, Mathilde R.; Inserra, Marco C.; Smith, Jennifer J.; Lewis, Richard J.; Alewood, Paul F.; Vetter, Irina; Dutertre, Sébastien

2015-01-01

Some venomous cone snails feed on small fishes using an immobilizing combination of synergistic venom peptides that target Kv and Nav channels. As part of this envenomation strategy, δ-conotoxins are potent ichtyotoxins that enhance Nav channel function. δ-Conotoxins belong to an ancient and widely distributed gene superfamily, but any evolutionary link from ancestral worm-eating cone snails to modern piscivorous species has not been elucidated. Here, we report the discovery of SuVIA, a potent vertebrate-active δ-conotoxin characterized from a vermivorous cone snail (Conus suturatus). SuVIA is equipotent at hNaV1.3, hNaV1.4 and hNaV1.6 with EC50s in the low nanomolar range. SuVIA also increased peak hNaV1.7 current by approximately 75% and shifted the voltage-dependence of activation to more hyperpolarized potentials from –15 mV to –25 mV, with little effect on the voltage-dependence of inactivation. Interestingly, the proximal venom gland expression and pain-inducing effect of SuVIA in mammals suggest that δ-conotoxins in vermivorous cone snails play a defensive role against higher order vertebrates. We propose that δ-conotoxins originally evolved in ancestral vermivorous cones to defend against larger predators including fishes have been repurposed to facilitate a shift to piscivorous behaviour, suggesting an unexpected underlying mechanism for this remarkable evolutionary transition. PMID:26156767

A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

PubMed Central

Leitwein, Maeva; Guinand, Bruno; Pouzadoux, Juliette; Desmarais, Erick; Berrebi, Patrick; Gagnaire, Pierre-Alexandre

2017-01-01

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout. PMID:28235829

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

PubMed

Johnston, Iain G; Williams, Ben P

2016-02-24

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

"Most people are simply not designed to eat pasta": evolutionary explanations for obesity in the low-carbohydrate diet movement.

PubMed

Knight, Christine

2011-09-01

Low-carbohydrate diets, notably the Atkins Diet, were particularly popular in Britain and North America in the late 1990s and early 2000s. On the basis of a discourse analysis of bestselling low-carbohydrate diet books, I examine and critique genetic and evolutionary explanations for obesity and diabetes as they feature in the low-carbohydrate literature. Low-carbohydrate diet books present two distinct neo-Darwinian explanations of health and body-weight. First, evolutionary nutrition is based on the premise that the human body has adapted to function best on the diet eaten in the Paleolithic era. Second, the thrifty gene theory suggests that feast-or-famine conditions during human evolutionary development naturally selected for people who could store excess energy as body fat for later use. However, the historical narratives and scientific arguments presented in the low-carbohydrate literature are beset with generalisations, inconsistencies and errors. These result, I argue, from the use of the primitive as a discursive "blank slate" onto which to project ideals perceived to be lacking in contemporary industrialised life.

Using evolutionary computation to optimize an SVM used in detecting buried objects in FLIR imagery

NASA Astrophysics Data System (ADS)

Paino, Alex; Popescu, Mihail; Keller, James M.; Stone, Kevin

2013-06-01

In this paper we describe an approach for optimizing the parameters of a Support Vector Machine (SVM) as part of an algorithm used to detect buried objects in forward looking infrared (FLIR) imagery captured by a camera installed on a moving vehicle. The overall algorithm consists of a spot-finding procedure (to look for potential targets) followed by the extraction of several features from the neighborhood of each spot. The features include local binary pattern (LBP) and histogram of oriented gradients (HOG) as these are good at detecting texture classes. Finally, we project and sum each hit into UTM space along with its confidence value (obtained from the SVM), producing a confidence map for ROC analysis. In this work, we use an Evolutionary Computation Algorithm (ECA) to optimize various parameters involved in the system, such as the combination of features used, parameters on the Canny edge detector, the SVM kernel, and various HOG and LBP parameters. To validate our approach, we compare results obtained from an SVM using parameters obtained through our ECA technique with those previously selected by hand through several iterations of "guess and check".

Testing co-evolutionary hypotheses over geological timescales: interactions between Mesozoic non-avian dinosaurs and cycads.

PubMed

Butler, Richard J; Barrett, Paul M; Kenrick, Paul; Penn, Malcolm G

2009-02-01

The significance of co-evolution over ecological timescales is well established, yet it remains unclear to what extent co-evolutionary processes contribute to driving large-scale evolutionary and ecological changes over geological timescales. Some of the most intriguing and pervasive long-term co-evolutionary hypotheses relate to proposed interactions between herbivorous non-avian dinosaurs and Mesozoic plants, including cycads. Dinosaurs have been proposed as key dispersers of cycad seeds during the Mesozoic, and temporal variation in cycad diversity and abundance has been linked to dinosaur faunal changes. Here we assess the evidence for proposed hypotheses of trophic and evolutionary interactions between these two groups using diversity analyses, a new database of Cretaceous dinosaur and plant co-occurrence data, and a geographical information system (GIS) as a visualisation tool. Phylogenetic evidence suggests that the origins of several key biological properties of cycads (e.g. toxins, bright-coloured seeds) likely predated the origin of dinosaurs. Direct evidence of dinosaur-cycad interactions is lacking, but evidence from extant ecosystems suggests that dinosaurs may plausibly have acted as seed dispersers for cycads, although it is likely that other vertebrate groups (e.g. birds, early mammals) also played a role. Although the Late Triassic radiations of dinosaurs and cycads appear to have been approximately contemporaneous, few significant changes in dinosaur faunas coincide with the late Early Cretaceous cycad decline. No significant spatiotemporal associations between particular dinosaur groups and cycads can be identified - GIS visualisation reveals disparities between the spatiotemporal distributions of some dinosaur groups (e.g. sauropodomorphs) and cycads that are inconsistent with co-evolutionary hypotheses. The available data provide no unequivocal support for any of the proposed co-evolutionary interactions between cycads and herbivorous dinosaurs - diffuse co-evolutionary scenarios that are proposed to operate over geological timescales are plausible, but such hypotheses need to be firmly grounded on direct evidence of interaction and may be difficult to support given the patchiness of the fossil record.

The evolutionary origin of the vertebrate body plan: the problem of head segmentation.

PubMed

Onai, Takayuki; Irie, Naoki; Kuratani, Shigeru

2014-01-01

The basic body plan of vertebrates, as typified by the complex head structure, evolved from the last common ancestor approximately 530 Mya. In this review, we present a brief overview of historical discussions to disentangle the various concepts and arguments regarding the evolutionary development of the vertebrate body plan. We then explain the historical transition of the arguments about the vertebrate body plan from merely epistemological comparative morphology to comparative embryology as a scientific treatment on this topic. Finally, we review the current progress of molecular evidence regarding the basic vertebrate body plan, focusing on the link between the basic vertebrate body plan and the evolutionarily conserved developmental stages (phylotypic stages).

Evolutionary rescue of a parasite population by mutation rate evolution.

PubMed

Greenspoon, Philip B; Mideo, Nicole

2017-10-01

The risk of antibiotic resistance evolution in parasites is a major problem for public health. Identifying factors which promote antibiotic resistance evolution is thus a priority in evolutionary medicine. The rate at which new mutations enter the parasite population is one important predictor; however, mutation rate is not necessarily a fixed quantity, as is often assumed, but can itself evolve. Here we explore the possible impacts of mutation rate evolution on the fate of a disease circulating in a host population, which is being treated with drugs, the use of which varies over time. Using an evolutionary rescue framework, we find that mutation rate evolution provides a dramatic increase in the probability that a parasite population survives treatment in only a limited region, while providing little or no advantage in other regions. Both epidemiological features, such as the virulence of infection, and population genetic parameters, such as recombination rate, play important roles in determining the probability of evolutionary rescue and whether mutation rate evolution enhances the probability of evolutionary rescue or not. While efforts to curtail mutation rate evolution in parasites may be worthwhile under some circumstances, our results suggest that this need not always be the case. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification

PubMed Central

Caetano-Anollés, Gustavo

2013-01-01

Reconstructing the evolutionary history of modern species is a difficult problem complicated by the conceptual and technical limitations of phylogenetic tree building methods. Here, we propose a comparative proteomic and functionomic inferential framework for genome evolution that allows resolving the tripartite division of cells and sketching their history. Evolutionary inferences were derived from the spread of conserved molecular features, such as molecular structures and functions, in the proteomes and functionomes of contemporary organisms. Patterns of use and reuse of these traits yielded significant insights into the origins of cellular diversification. Results uncovered an unprecedented strong evolutionary association between Bacteria and Eukarya while revealing marked evolutionary reductive tendencies in the archaeal genomic repertoires. The effects of nonvertical evolutionary processes (e.g., HGT, convergent evolution) were found to be limited while reductive evolution and molecular innovation appeared to be prevalent during the evolution of cells. Our study revealed a strong vertical trace in the history of proteins and associated molecular functions, which was reliably recovered using the comparative genomics approach. The trace supported the existence of a stem line of descent and the very early appearance of Archaea as a diversified superkingdom, but failed to uncover a hidden canonical pattern in which Bacteria was the first superkingdom to deploy superkingdom-specific structures and functions. PMID:24492748

Identification and Characterization of MYC Regulatory Elements: Links to Prostate Cancer

DTIC Science & Technology

2011-06-01

cell proliferation and growth,MYC is up-regulated at both the mRNA and protein levels in aggressive prostate cancers ( DeMarzo et al. 2003). In...evolutionary synthesis: A genetic theory of morphological evolution. Cell 134: 25–36. DeMarzo AM, Nelson WG, Isaacs WB, Epstein JI. 2003. Pathological and

The Role of Defeat and Entrapment in Depression, Anxiety, and Suicide

ERIC Educational Resources Information Center

Taylor, Peter James; Gooding, Patricia; Wood, Alex M.; Tarrier, Nicholas

2011-01-01

Defeat and entrapment are psychological constructs that have played a central role in evolutionary accounts of depression. These concepts have since been implicated in theoretical accounts of anxiety disorders and suicidality. The current article reports on a systematic review of the existing research investigating the links among defeat,…

Toward a Coevolution of Language Theories: Linking Composition with Brain and Language Studies.

ERIC Educational Resources Information Center

Adkison, Stephen

Focusing specifically on the theories offered by language development theorist L. S. Vygotsky and evolutionary theorist Terrence Deacon, this paper examines the ways in which theories of language in composition studies coincide and differ with the theories currently being researched in neurobiology and physical anthropology. This examination…

A Missing Link To Understanding Evolution.

ERIC Educational Resources Information Center

Chandler, Pauline

1997-01-01

Describes an activity in which students assume the roles of scientists living in the year 2,001,997 and make their own fossil record discoveries of animals that have undergone evolutionary changes since 1997. Students choose the animals as well as create the adaptations that have taken place. Includes a sample scoring rubric. (DKM)

Evolutionary perspectives on emotions and their link to intentions, dispositions and behavior. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Wildgruber, Dirk; Kreifelts, Benjamin

2015-06-01

Koelsch and coworkers present a sophisticated neuroanatomical model of emotions comprising four affect-systems and four output-systems, each bound to a specific brain area [1]. Moreover, they suggest the emergence of distinct components of subjective feelings or "emotion percepts" due to integration of the activation across these subsystems. Incorporating numerous neurobiological, psychological and philosophical findings on human emotions, the model reflects an extensive interdisciplinary approach. Considering an evolutionary perspective, however, we would like to address some issues concerning emotions and their link to intentions, dispositions and behavior that are not fully covered by the Quartet Model. Charles Darwin pointed out that individuals that are better adapted to their environment have increased chances of survival and reproduction. Therefore, natural selection leads to a rising prevalence of properties offering a survival benefit across generations [2]. To better understand the biological functions of emotions we propose to ask the question: How do emotions provide a benefit for survival and reproduction?

Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats.

PubMed

Teske, Peter R; Beheregaray, Luciano B

2009-08-23

Seahorses (Syngnathidae: Hippocampus) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses' upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species.

Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arbing, Mark A.; Handelman, Samuel K.; Kuzin, Alexandre P.

2010-09-27

Bacterial toxin-antitoxin (TA) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. Sequence analyses suggest that TA families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different TA families. Our crystal structures of Phd-Doc from bacteriophage P1, the HigA antitoxin from Escherichia coli CFT073, and YeeU of the YeeUWV systems from E. coli K12 and Shigella flexneri confirm this inference and reveal additional, unanticipated structural relationships. The growth-regulating Doc toxin exhibits structural similarity to secreted virulence factors that are toxic for eukaryotic target cells. The Phdmore » antitoxin possesses the same fold as both the YefM and NE2111 antitoxins that inhibit structurally unrelated toxins. YeeU, which has an antitoxin-like activity that represses toxin expression, is structurally similar to the ribosome-interacting toxins YoeB and RelE. These observations suggest extensive functional exchanges have occurred between TA systems during bacterial evolution.« less

A Tale of Four Stories: Soil Ecology, Theory, Evolution and the Publication System

PubMed Central

Barot, Sébastien; Blouin, Manuel; Fontaine, Sébastien; Jouquet, Pascal; Lata, Jean-Christophe; Mathieu, Jérôme

2007-01-01

Background Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. Findings We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. Conclusion This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary. PMID:18043755

Phylogenetic estimates of diversification rate are affected by molecular rate variation.

PubMed

Duchêne, D A; Hua, X; Bromham, L

2017-10-01

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Evolutionary genomics: is Buchnera a bacterium or an organelle?

PubMed

Andersson, J O

2000-11-30

The first genome sequence of an intracellular bacterial symbiont of a eukaryotic cell has been determined. The Buchnera genome shares features with the genomes of both intracellular pathogenic bacteria and eukaryotic organelles, and it may represent an intermediate between the two.

The Morphologic Evolution of the Amazon Coastal Plain, Cabo Norte, Amapa, Brazil: The Need for Integrated Investigation on the Internal Continental Shelf.

NASA Astrophysics Data System (ADS)

Silveira, O.; Santos, V. F.; Takiyama, L. R.

2007-05-01

The north brazilian coastal region is submitted to the conjunction of three major forcing: 1) Atmospheric, related to the wind and precipitation regimen and controlling the climatic seasonality and the local rivers hydrology; 2) Oceanic, result of the general oceanic circulation (North Equatorial Current-NEC) and it modulation with the atmospheric forcing (North Brazilian Coastal Current reflection), and 3) Amazonic, which is a result of the sedimentary transport from Amazon river, being itself under the influence of the atmospheric and oceanic forcing. Their main characteristic are the proper periodicities and also variabilities expressed according multiples and differentiated scales of time and space, determining the structure and functioning of the coastal space, giving to the Amazon coast line a considerable environmental instability. The Amapa Coastal Plain shows important part of this environmental instability. Semidiurnal macro tides, strong currents and tidal bores acts over a low gradient coastal plain which evolutionary process are intrinsically related with tectonic and geological settings. Two main areas can be distinguished in this scenario. The first one is the Amapa Lakes Region, developed over meanders of ancient drainages building a mosaic of low relief forms, with varied shapes, linked throughout communication channels. Two lacustrine belts showing alignments with the main tectonic traces were recognized beginning at the internal limit of the coastal plain, flowing southeast through the Tabaco Creek until reach the Araguari River. In it way it conform the Occidental and Meridional Belts represented by shallow lakes, totally dependent of Tartarugal River discharge and surrounded by enormous areas of peat highly sensitive to fire during the regional low discharge. Light blue clays, peat and a package of tidal deposits with fluidization structures were recognized close to Araguari River, suggesting deposition during high sea level. The second area refers to the coastal zone between the Amapa Grande River and Araguari River, including Maraca Island and the Oriental lacustrine Belt. Westward the island, at least three paleolevels of clays with roots in life position suggests regressive/transgressive events. Extraordinaty paleodrainage network beginnig at the continent and recognized at the insular portion suggests links with the paleochannels found at the continental shelf. The Oriental Belt of lakes is located close to the coastline, at Cabo Norte. It main feature is a mud lump approximately 10 Km ratio, well recognized at the remote sensing. It shows similar evolutionary processes with Araguari River, dating from XIX century, when this river had two mouths defined by the Carpori Island. The reasons of the deactivation are still unknowed, but, this rapid morphological evolution indicates short time colmatation processes that can be linked to tectonic regional processes. On the other hand, the Cabo Norte feature consolidation may impose changes in the sedimentation processes yielding space reduction over the coastal plain accumulation, diminishing of the solid and liquid fluvial discharge and promoting the availability of the local sediment transport over the littoral. The investigation of these processes requires an integrated coastal plain-continental shelf morphological study applying adequate techniques for modification studies and dating ages over short geological time frame, in century scale level.

Evolution of auroral acceleration region field-aligned current systems, plasma, and potentials observed by Cluster during substorms

NASA Astrophysics Data System (ADS)

Hull, A. J.; Chaston, C. C.; Fillingim, M. O.; Frey, H. U.; Goldstein, M. L.; Bonnell, J. W.; Mozer, F.

2015-12-01

The auroral acceleration region is an integral link in the chain of events that transpire during substorms, and the currents, plasma and electric fields undergo significant changes driven by complex dynamical processes deep in the magnetotail. The acceleration processes that occur therein accelerate and heat the plasma that ultimately leads to some of the most intense global substorm auroral displays. Though this region has garnered considerable attention, the temporal evolution of field-aligned current systems, associated acceleration processes, and resultant changes in the plasma constituents that occur during key stages of substorm development remain unclear. In this study we present a survey of Cluster traversals within and just above the auroral acceleration region (≤3 Re altitude) during substorms. Particular emphasis is on the spatial morphology and developmental sequence of auroral acceleration current systems, potentials and plasma constituents, with the aim of identifying controlling factors, and assessing auroral emmission consequences. Exploiting multi-point measurements from Cluster in combination with auroral imaging, we reveal the injection powered, Alfvenic nature of both the substorm onset and expansion of auroral particle acceleration. We show evidence that indicates substorm onsets are characterized by the gross-intensification and filamentation/striation of pre-existing large-scale current systems to smaller/dispersive scale Alfven waves. Such an evolutionary sequence has been suggested in theoretical models or single spacecraft data, but has not been demonstrated or characterized in multispacecraft observations until now. It is also shown how the Alfvenic variations over time may dissipate to form large-scale inverted-V structures characteristic of the quasi-static aurora. These findings suggest that, in addition to playing active roles in driving substorm aurora, inverted-V and Alfvenic acceleration processes are causally linked. Key elements of substorm current spatial structure and temporal development, relationship to electric fields/potentials, plasma moment and distribution features, causal linkages to auroral emission features, and other properties will be discussed.

Childhood maltreatment and its link to borderline personality disorder features in children: A systematic review approach.

PubMed

Ibrahim, Jeyda; Cosgrave, Nicola; Woolgar, Matthew

2018-01-01

Borderline personality disorder has repeatedly been associated with a history of maltreatment in childhood; however, research on maltreatment and its link to borderline features in children is limited. The aim of this review is to synthesise the existing data on the association between maltreatment and borderline features in childhood. In total, 10 studies were included in this systematic review. Studies indicated that children with borderline features were more likely to have a history of maltreatment, and that children who had been maltreated were more likely to present with borderline features. Other risk factors such as cognitive and executive functioning deficits, parental dysfunction and genetic vulnerability were also identified across studies. This review adds to the literature by highlighting maltreatment as a risk factor for borderline features in childhood. Longitudinal research is required to establish the link between childhood borderline features and adult borderline features. Implications for early identification, prevention and intervention services are discussed.

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

PubMed Central

Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

2009-01-01

Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability. PMID:19630942

Foundational errors in the Neutral and Nearly-Neutral theories of evolution in relation to the Synthetic Theory: is a new evolutionary paradigm necessary?

PubMed

Valenzuela, Carlos Y

2013-01-01

The Neutral Theory of Evolution (NTE) proposes mutation and random genetic drift as the most important evolutionary factors. The most conspicuous feature of evolution is the genomic stability during paleontological eras and lack of variation among taxa; 98% or more of nucleotide sites are monomorphic within a species. NTE explains this homology by random fixation of neutral bases and negative selection (purifying selection) that does not contribute either to evolution or polymorphisms. Purifying selection is insufficient to account for this evolutionary feature and the Nearly-Neutral Theory of Evolution (N-NTE) included negative selection with coefficients as low as mutation rate. These NTE and N-NTE propositions are thermodynamically (tendency to random distributions, second law), biotically (recurrent mutation), logically and mathematically (resilient equilibria instead of fixation by drift) untenable. Recurrent forward and backward mutation and random fluctuations of base frequencies alone in a site make life organization and fixations impossible. Drift is not a directional evolutionary factor, but a directional tendency of matter-energy processes (second law) which threatens the biotic organization. Drift cannot drive evolution. In a site, the mutation rates among bases and selection coefficients determine the resilient equilibrium frequency of bases that genetic drift cannot change. The expected neutral random interaction among nucleotides is zero; however, huge interactions and periodicities were found between bases of dinucleotides separated by 1, 2... and more than 1,000 sites. Every base is co-adapted with the whole genome. Neutralists found that neutral evolution is independent of population size (N); thus neutral evolution should be independent of drift, because drift effect is dependent upon N. Also, chromosome size and shape as well as protein size are far from random.

Phylogeny of Selaginellaceae: There is value in morphology after all!

PubMed

Weststrand, Stina; Korall, Petra

2016-12-01

The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian-Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions. © 2016 Weststrand and Korall. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY 4.0).

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.

PubMed

Bosi, Emanuele; Fondi, Marco; Orlandini, Valerio; Perrin, Elena; Maida, Isabel; de Pascale, Donatella; Tutino, Maria Luisa; Parrilli, Ermenegilda; Lo Giudice, Angelina; Filloux, Alain; Fani, Renato

2017-01-17

Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.

Maturation experiments reveal bias in the fossil record of feathers

NASA Astrophysics Data System (ADS)

McNamara, Maria; Field, Daniel

2016-04-01

The evolutionary history of birds and feathers is a major focus in palaeobiology and evolutionary biology. Diverse exceptionally preserved birds and feathered dinosaurs from Jurassic and Cretaceous biotas in China have provided pivotal evidence of early feathers and feather-like integumentary features, but the true nature of many of these fossil soft tissues is still debated. Interpretations of feathers at intermediate developmental stages (i.e. Stages II, III and IV) and of simple quill-like (Stage I) feathers are particularly controversial. This reflects key uncertainties relating to the preservation potential of feathers at different evolutionary-developmental stages, and to the relative preservation potential of diagnostic features of Stage I feathers and hair. To resolve these issues, we used high pressure-high temperature autoclave experiments to simulate the effects of burial on modern feathers from the Black Coucal (Centropus grilii) and Common Starling (Sturnus vulgaris), and on human hair. Our results reveal profound differences in the recalcitrance of feathers of different types during maturation: Stage I and Stage V feathers retain diagnostic morphological and ultrastructural details following maturation, whereas other feather types do not. Further, the morphology and arrangement of certain ultrastructural features diagnostic of Stages III and IV, e.g. barbules, are preferentially lost during maturation. These results indicate a pervasive bias in the fossil record of feathers, whereby preservation of feathers at Stages I and V is favored. Critical stages in the evolution of feathers, i.e. Stages II, III and IV, are less likely to be preserved and more likely to be misinterpreted as feathers at earlier developmental stages. Our discovery has major implications for our understanding of the fidelity of the fossil record of feathers and provides a framework for testing the significance of putative examples of fossil feathers at different developmental stages.

How could language have evolved?

PubMed

Bolhuis, Johan J; Tattersall, Ian; Chomsky, Noam; Berwick, Robert C

2014-08-01

The evolution of the faculty of language largely remains an enigma. In this essay, we ask why. Language's evolutionary analysis is complicated because it has no equivalent in any nonhuman species. There is also no consensus regarding the essential nature of the language "phenotype." According to the "Strong Minimalist Thesis," the key distinguishing feature of language (and what evolutionary theory must explain) is hierarchical syntactic structure. The faculty of language is likely to have emerged quite recently in evolutionary terms, some 70,000-100,000 years ago, and does not seem to have undergone modification since then, though individual languages do of course change over time, operating within this basic framework. The recent emergence of language and its stability are both consistent with the Strong Minimalist Thesis, which has at its core a single repeatable operation that takes exactly two syntactic elements a and b and assembles them to form the set {a, b}.

How Could Language Have Evolved?

PubMed Central

Bolhuis, Johan J.; Tattersall, Ian; Chomsky, Noam; Berwick, Robert C.

2014-01-01

The evolution of the faculty of language largely remains an enigma. In this essay, we ask why. Language's evolutionary analysis is complicated because it has no equivalent in any nonhuman species. There is also no consensus regarding the essential nature of the language “phenotype.” According to the “Strong Minimalist Thesis,” the key distinguishing feature of language (and what evolutionary theory must explain) is hierarchical syntactic structure. The faculty of language is likely to have emerged quite recently in evolutionary terms, some 70,000–100,000 years ago, and does not seem to have undergone modification since then, though individual languages do of course change over time, operating within this basic framework. The recent emergence of language and its stability are both consistent with the Strong Minimalist Thesis, which has at its core a single repeatable operation that takes exactly two syntactic elements a and b and assembles them to form the set {a, b}. PMID:25157536

A survey on evolutionary algorithm based hybrid intelligence in bioinformatics.

PubMed

Li, Shan; Kang, Liying; Zhao, Xing-Ming

2014-01-01

With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs) are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

Clouds on Neptune: Motions, Evolution, and Structure

NASA Technical Reports Server (NTRS)

Sromovsky, Larry A.; Morgan, Thomas (Technical Monitor)

2001-01-01

The aims of our original proposal were these: (1) improving measurements of Neptune's circulation, (2) understanding the spatial distribution of cloud features, (3) discovery of new cloud features and understanding their evolutionary process, (4) understanding the vertical structure of zonal cloud patterns, (5) defining the structure of discrete cloud features, and (6) defining the near IR albedo and light curve of Triton. Towards these aims we proposed analysis of existing 1996 groundbased NSFCAM/IRTF observations and nearly simultaneous WFPC2 observations from the Hubble Space Telescope. We also proposed to acquire new observations from both HST and the IRTF.

Influence of different positive emotions on persuasion processing: a functional evolutionary approach.

PubMed

Griskevicius, Vladas; Shiota, Michelle N; Neufeld, Samantha L

2010-04-01

Much research has found that positive affect facilitates increased reliance on heuristics in cognition. However, theories proposing distinct evolutionary fitness-enhancing functions for specific positive emotions also predict important differences among the consequences of different positive emotion states. Two experiments investigated how six positive emotions influenced the processing of persuasive messages. Using different methods to induce emotions and assess processing, we showed that the positive emotions of anticipatory enthusiasm, amusement, and attachment love tended to facilitate greater acceptance of weak persuasive messages (consistent with previous research), whereas the positive emotions of awe and nurturant love reduced persuasion by weak messages. In addition, a series of mediation analyses suggested that the effects distinguishing different positive emotions from a neutral control condition were best accounted for by different mediators rather than by one common mediator. These findings build upon approaches that link affective valence to certain types of processing, documenting emotion-specific effects on cognition that are consistent with functional evolutionary accounts of discrete positive emotions. Copyright 2010 APA, all rights reserved.

The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses.

PubMed

Hummel, Barbara; Hansen, Erik C; Yoveva, Aneliya; Aprile-Garcia, Fernando; Hussong, Rebecca; Sawarkar, Ritwick

2017-03-01

Understanding how genotypes are linked to phenotypes is important in biomedical and evolutionary studies. The chaperone heat-shock protein 90 (HSP90) buffers genetic variation by stabilizing proteins with variant sequences, thereby uncoupling phenotypes from genotypes. Here we report an unexpected role of HSP90 in buffering cis-regulatory variation affecting gene expression. By using the tripartite-motif-containing 28 (TRIM28; also known as KAP1)-mediated epigenetic pathway, HSP90 represses the regulatory influence of endogenous retroviruses (ERVs) on neighboring genes that are critical for mouse development. Our data based on natural variations in the mouse genome show that genes respond to HSP90 inhibition in a manner dependent on their genomic location with regard to strain-specific ERV-insertion sites. The evolutionary-capacitor function of HSP90 may thus have facilitated the exaptation of ERVs as key modifiers of gene expression and morphological diversification. Our findings add a new regulatory layer through which HSP90 uncouples phenotypic outcomes from individual genotypes.

Animal behaviour and algal camouflage jointly structure predation and selection.

PubMed

Start, Denon

2018-05-01

Trait variation can structure interactions between individuals, thus shaping selection. Although antipredator strategies are an important component of many aquatic systems, how multiple antipredator traits interact to influence consumption and selection remains contentious. Here, I use a common larval dragonfly (Epitheca canis) and its predator (Anax junius) to test for the joint effects of activity rate and algal camouflage on predation and survival selection. I found that active and poorly camouflaged Epitheca were more likely to be consumed, and thus, survival selection favoured inactive and well-camouflaged individuals. Notably, camouflage dampened selection on activity rate, likely by reducing attack rates when Epitheca encountered a predator. Correlational selection is therefore conferred by the ecological interaction of traits, rather than by opposing selection acting on linked traits. I suggest that antipredator traits with different adaptive functions can jointly structure patterns of consumption and selection. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Lifemap: Exploring the Entire Tree of Life.

PubMed

de Vienne, Damien M

2016-12-01

The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms.

Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations

PubMed Central

Bershtein, Shimon; Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

2016-01-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. PMID:27810574

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

PubMed

Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

2017-02-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Establishment of the mathematical model for diagnosing the engine valve faults by genetic programming

NASA Astrophysics Data System (ADS)

Yang, Wen-Xian

2006-05-01

Available machine fault diagnostic methods show unsatisfactory performances on both on-line and intelligent analyses because their operations involve intensive calculations and are labour intensive. Aiming at improving this situation, this paper describes the development of an intelligent approach by using the Genetic Programming (abbreviated as GP) method. Attributed to the simple calculation of the mathematical model being constructed, different kinds of machine faults may be diagnosed correctly and quickly. Moreover, human input is significantly reduced in the process of fault diagnosis. The effectiveness of the proposed strategy is validated by an illustrative example, in which three kinds of valve states inherent in a six-cylinders/four-stroke cycle diesel engine, i.e. normal condition, valve-tappet clearance and gas leakage faults, are identified. In the example, 22 mathematical functions have been specially designed and 8 easily obtained signal features are used to construct the diagnostic model. Different from existing GPs, the diagnostic tree used in the algorithm is constructed in an intelligent way by applying a power-weight coefficient to each feature. The power-weight coefficients vary adaptively between 0 and 1 during the evolutionary process. Moreover, different evolutionary strategies are employed, respectively for selecting the diagnostic features and functions, so that the mathematical functions are sufficiently utilized and in the meantime, the repeated use of signal features may be fully avoided. The experimental results are illustrated diagrammatically in the following sections.

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

PubMed Central

Mohammed, Jaaved; Flynt, Alex S.; Siepel, Adam; Lai, Eric C.

2013-01-01

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class. PMID:23882112

LinkFinder: An expert system that constructs phylogenic trees

NASA Technical Reports Server (NTRS)

Inglehart, James; Nelson, Peter C.

1991-01-01

An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time.

Protein self-marking by ectoparasites: a case study using bed bugs

USDA-ARS?s Scientific Manuscript database

1. The ability to mark individuals is a critical feature of many ecological and evolutionary investigations, including dispersal studies. Insect dispersal is generally investigated using mark-release-recapture techniques, whereby marked individuals are released at a known location and then captured ...

Comparative Cognitive Development

ERIC Educational Resources Information Center

Matsuzawa, Tetsuro

2007-01-01

This paper aims to compare cognitive development in humans and chimpanzees to illuminate the evolutionary origins of human cognition. Comparison of morphological data and life history strongly highlights the common features of all primate species, including humans. The human mother-infant relationship is characterized by the physical separation of…

Adaptive classifier for steel strip surface defects

NASA Astrophysics Data System (ADS)

Jiang, Mingming; Li, Guangyao; Xie, Li; Xiao, Mang; Yi, Li

2017-01-01

Surface defects detection system has been receiving increased attention as its precision, speed and less cost. One of the most challenges is reacting to accuracy deterioration with time as aged equipment and changed processes. These variables will make a tiny change to the real world model but a big impact on the classification result. In this paper, we propose a new adaptive classifier with a Bayes kernel (BYEC) which update the model with small sample to it adaptive for accuracy deterioration. Firstly, abundant features were introduced to cover lots of information about the defects. Secondly, we constructed a series of SVMs with the random subspace of the features. Then, a Bayes classifier was trained as an evolutionary kernel to fuse the results from base SVMs. Finally, we proposed the method to update the Bayes evolutionary kernel. The proposed algorithm is experimentally compared with different algorithms, experimental results demonstrate that the proposed method can be updated with small sample and fit the changed model well. Robustness, low requirement for samples and adaptive is presented in the experiment.

The interactions of ants with their biotic environment.

PubMed

Chomicki, Guillaume; Renner, Susanne S

2017-03-15

This s pecial feature results from the symposium 'Ants 2016: ant interactions with their biotic environments' held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this s pecial feature After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts. Using a large molecular clock-dated Formicidae phylogeny, we map the evolutionary origins of different ant clades' interactions with plants, fungi and hemiptera. Ants' biotic interactions provide ideal systems to address fundamental ecological and evolutionary questions about mutualism, coevolution, adaptation and animal communication. © 2017 The Author(s).

The interactions of ants with their biotic environment

PubMed Central

Renner, Susanne S.

2017-01-01

This special feature results from the symposium ‘Ants 2016: ant interactions with their biotic environments’ held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this special feature. After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts. Using a large molecular clock-dated Formicidae phylogeny, we map the evolutionary origins of different ant clades' interactions with plants, fungi and hemiptera. Ants' biotic interactions provide ideal systems to address fundamental ecological and evolutionary questions about mutualism, coevolution, adaptation and animal communication. PMID:28298352

A Simple Mathematical Model Inspired by the Purkinje Cells: From Delayed Travelling Waves to Fractional Diffusion.

PubMed

Dipierro, Serena; Valdinoci, Enrico

2018-07-01

Recently, several experiments have demonstrated the existence of fractional diffusion in the neuronal transmission occurring in the Purkinje cells, whose malfunctioning is known to be related to the lack of voluntary coordination and the appearance of tremors. Also, a classical mathematical feature is that (fractional) parabolic equations possess smoothing effects, in contrast with the case of hyperbolic equations, which typically exhibit shocks and discontinuities. In this paper, we show how a simple toy-model of a highly ramified structure, somehow inspired by that of the Purkinje cells, may produce a fractional diffusion via the superposition of travelling waves that solve a hyperbolic equation. This could suggest that the high ramification of the Purkinje cells might have provided an evolutionary advantage of "smoothing" the transmission of signals and avoiding shock propagations (at the price of slowing a bit such transmission). Although an experimental confirmation of the possibility of such evolutionary advantage goes well beyond the goals of this paper, we think that it is intriguing, as a mathematical counterpart, to consider the time fractional diffusion as arising from the superposition of delayed travelling waves in highly ramified transmission media. The case of a travelling concave parabola with sufficiently small curvature is explicitly computed. The new link that we propose between time fractional diffusion and hyperbolic equation also provides a novelty with respect to the usual paradigm relating time fractional diffusion with parabolic equations in the limit. This paper is written in such a way as to be of interest to both biologists and mathematician alike. In order to accomplish this aim, both complete explanations of the objects considered and detailed lists of references are provided.

A hypothesis linking chrysophyte microfossils to lake carbon dynamics on ecological and evolutionary time scales

NASA Astrophysics Data System (ADS)

Wolfe, Alexander P.; Siver, Peter A.

2013-12-01

Chrysophyte algae are common in the plankton of oligotrophic lakes and produce a rich microfossil record of siliceous cysts and scales. Paleolimnological investigations and phytoplankton records suggest that chrysophyte populations are increasing in a wide range of boreal and arctic lakes, ultimately representing one component of the limnological response to contemporary global changes. However, the exact mechanisms responsible for widespread increases of chrysophyte populations remain elusive. We hypothesize that recent increases in chrysophytes are related to rising pCO2 in lakes, in part because these algae lack carbon concentrating mechanisms and therefore rely on diffusive entry of CO2 to Rubisco during photosynthesis. We assessed the abundance of modern sediment chrysophyte microfossils in relation to summer CO2 relative saturation in 46 New England (USA) lakes, revealing significant positive relationships for both cysts and scales. These observations imply that correlations between chrysophytes and limnological conditions including low pH, oligotrophy, and elevated dissolved organic matter are ultimately underscored by the high pCO2 associated with these conditions. In lakes where chrysophyte populations have expanded over recent decades, we infer that increasingly heterotrophic conditions with respect to CO2 have stimulated production by these organisms. This linkage is supported by the remarkable abundance and diversity of chrysophytes from middle Eocene lake sediments, deposited under atmospheric CO2 concentrations significantly higher than present. The Eocene assemblages suggest that any chrysophyte-CO2 connection borne out of results from modern and sub-recent sediments also operated on evolutionary time scales, and thus the absence of carbon concentrating mechanisms appears to be an ancient feature within the group. Chrysophyte microfossils may potentially provide important insights concerning the temporal dynamics of carbon cycling in aquatic ecosystems.

The evolution of hyperactivity, impulsivity and cognitive diversity

PubMed Central

Williams, Jonathan; Taylor, Eric

2005-01-01

The evolutionary status of attention deficit/hyperactivity disorder (ADHD) is central to assessments of whether modern society has created it, either physically or socially; and is potentially useful in understanding its neurobiological basis and treatment. The high prevalence of ADHD (5–10%) and its association with the seven-repeat allele of DRD4, which is positively selected in evolution, raise the possibility that ADHD increases the reproductive fitness of the individual, and/or the group. However, previous suggestions of evolutionary roles for ADHD have not accounted for its confinement to a substantial minority. Because one of the key features of ADHD is its diversity, and many benefits of population diversity are well recognized (as in immunity), we study the impact of groups' behavioural diversity on their fitness. Diversity occurs along many dimensions, and for simplicity we choose unpredictability (or variability), excess of which is a well-established characteristic of ADHD. Simulations of the Changing Food group task show that unpredictable behaviour by a minority optimizes results for the group. Characteristics of such group exploration tasks are risk-taking, in which costs are borne mainly by the individual; and information-sharing, in which benefits accrue to the entire group. Hence, this work is closely linked to previous studies of evolved altruism. We conclude that even individually impairing combinations of genes, such as ADHD, can carry specific benefits for society, which can be selected for at that level, rather than being merely genetic coincidences with effects confined to the individual. The social benefits conferred by diversity occur both inside and outside the ‘normal’ range, and these may be distinct. This view has the additional merit of offering explanations for the prevalence, sex and age distribution, severity distribution and heterogeneity of ADHD. PMID:16849269

Investigating the Geological History of Asteroid 101955 Bennu Through Remote Sensing and Returned Sample Analyses

NASA Technical Reports Server (NTRS)

Messenger, S.; Connolly, H. C., Jr.; Lauretta, D. S.; Bottke, W. F.

2014-01-01

The NASA New Frontiers Mission OSRIS-REx will return surface regolith samples from near-Earth asteroid 101955 Bennu in September 2023. This target is classified as a B-type asteroid and is spectrally similar to CI and CM chondrite meteorites [1]. The returned samples are thus expected to contain primitive ancient Solar System materials that formed in planetary, nebular, interstellar, and circumstellar environments. Laboratory studies of primitive astromaterials have yielded detailed constraints on the origins, properties, and evolutionary histories of a wide range of Solar System bodies. Yet, the parent bodies of meteorites and cosmic dust are generally unknown, genetic and evolutionary relationships among asteroids and comets are unsettled, and links between laboratory and remote observations remain tenuous. The OSIRIS-REx mission will offer the opportunity to coordinate detailed laboratory analyses of asteroidal materials with known and well characterized geological context from which the samples originated. A primary goal of the OSIRIS-REx mission will be to provide detailed constraints on the origin and geological and dynamical history of Bennu through coordinated analytical studies of the returned samples. These microanalytical studies will be placed in geological context through an extensive orbital remote sensing campaign that will characterize the global geological features and chemical diversity of Bennu. The first views of the asteroid surface and of the returned samples will undoubtedly bring remarkable surprises. However, a wealth of laboratory studies of meteorites and spacecraft encounters with primitive bodies provides a useful framework to formulate priority scientific questions and effective analytical approaches well before the samples are returned. Here we summarize our approach to unraveling the geological history of Bennu through returned sample analyses.

Evolutionary history and leaf succulence as explanations for medicinal use in aloes and the global popularity of Aloe vera.

PubMed

Grace, Olwen M; Buerki, Sven; Symonds, Matthew R E; Forest, Félix; van Wyk, Abraham E; Smith, Gideon F; Klopper, Ronell R; Bjorå, Charlotte S; Neale, Sophie; Demissew, Sebsebe; Simmonds, Monique S J; Rønsted, Nina

2015-02-26

Aloe vera supports a substantial global trade yet its wild origins, and explanations for its popularity over 500 related Aloe species in one of the world's largest succulent groups, have remained uncertain. We developed an explicit phylogenetic framework to explore links between the rich traditions of medicinal use and leaf succulence in aloes. The phylogenetic hypothesis clarifies the origins of Aloe vera to the Arabian Peninsula at the northernmost limits of the range for aloes. The genus Aloe originated in southern Africa ~16 million years ago and underwent two major radiations driven by different speciation processes, giving rise to the extraordinary diversity known today. Large, succulent leaves typical of medicinal aloes arose during the most recent diversification ~10 million years ago and are strongly correlated to the phylogeny and to the likelihood of a species being used for medicine. A significant, albeit weak, phylogenetic signal is evident in the medicinal uses of aloes, suggesting that the properties for which they are valued do not occur randomly across the branches of the phylogenetic tree. Phylogenetic investigation of plant use and leaf succulence among aloes has yielded new explanations for the extraordinary market dominance of Aloe vera. The industry preference for Aloe vera appears to be due to its proximity to important historic trade routes, and early introduction to trade and cultivation. Well-developed succulent leaf mesophyll tissue, an adaptive feature that likely contributed to the ecological success of the genus Aloe, is the main predictor for medicinal use among Aloe species, whereas evolutionary loss of succulence tends to be associated with losses of medicinal use. Phylogenetic analyses of plant use offer potential to understand patterns in the value of global plant diversity.

Marine Microbial Secondary Metabolites: Pathways, Evolution and Physiological Roles.

PubMed

Giordano, Daniela; Coppola, Daniela; Russo, Roberta; Denaro, Renata; Giuliano, Laura; Lauro, Federico M; di Prisco, Guido; Verde, Cinzia

2015-01-01

Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology. © 2015 Elsevier Ltd. All rights reserved.

Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects.

PubMed

Raimondi, Daniele; Gazzo, Andrea M; Rooman, Marianne; Lenaerts, Tom; Vranken, Wim F

2016-06-15

There are now many predictors capable of identifying the likely phenotypic effects of single nucleotide variants (SNVs) or short in-frame Insertions or Deletions (INDELs) on the increasing amount of genome sequence data. Most of these predictors focus on SNVs and use a combination of features related to sequence conservation, biophysical, and/or structural properties to link the observed variant to either neutral or disease phenotype. Despite notable successes, the mapping between genetic variants and their phenotypic effects is riddled with levels of complexity that are not yet fully understood and that are often not taken into account in the predictions, despite their promise of significantly improving the prediction of deleterious mutants. We present DEOGEN, a novel variant effect predictor that can handle both missense SNVs and in-frame INDELs. By integrating information from different biological scales and mimicking the complex mixture of effects that lead from the variant to the phenotype, we obtain significant improvements in the variant-effect prediction results. Next to the typical variant-oriented features based on the evolutionary conservation of the mutated positions, we added a collection of protein-oriented features that are based on functional aspects of the gene affected. We cross-validated DEOGEN on 36 825 polymorphisms, 20 821 deleterious SNVs, and 1038 INDELs from SwissProt. The multilevel contextualization of each (variant, protein) pair in DEOGEN provides a 10% improvement of MCC with respect to current state-of-the-art tools. The software and the data presented here is publicly available at http://ibsquare.be/deogen : wvranken@vub.ac.be Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evolution of floral diversity: genomics, genes and gamma

PubMed Central

Berger, Brent A.; Howarth, Dianella G.; Soltis, Douglas E.

2017-01-01

A salient feature of flowering plant diversification is the emergence of a novel suite of floral features coinciding with the origin of the most species-rich lineage, Pentapetalae. Advances in phylogenetics, developmental genetics and genomics, including new analyses presented here, are helping to reconstruct the specific evolutionary steps involved in the evolution of this clade. The enormous floral diversity among Pentapetalae appears to be built on a highly conserved ground plan of five-parted (pentamerous) flowers with whorled phyllotaxis. By contrast, lability in the number and arrangement of component parts of the flower characterize the early-diverging eudicot lineages subtending Pentapetalae. The diversification of Pentapetalae also coincides closely with ancient hexaploidy, referred to as the gamma whole-genome triplication, for which the phylogenetic timing, mechanistic details and molecular evolutionary consequences are as yet not fully resolved. Transcription factors regulating floral development often persist in duplicate or triplicate in gamma-derived genomes, and both individual genes and whole transcriptional programmes exhibit a shift from broadly overlapping to tightly defined expression domains in Pentapetalae flowers. Investigations of these changes associated with the origin of Pentapetalae can lead to a more comprehensive understanding of what is arguably one of the most important evolutionary diversification events within terrestrial plants. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994132

Independent evolution of genomic characters during major metazoan transitions.

PubMed

Simakov, Oleg; Kawashima, Takeshi

2017-07-15

Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages. In this review we describe recent advances in our understanding of ancestral metazoan coding and non-coding features, as deduced from genomic comparisons. Some genomic changes such as innovations in gene and linkage content occur at different rates across metazoan clades, suggesting some level of independence among genomic characters. While their contribution to biological innovation remains largely unclear, we review recent literature about certain genomic changes that do correlate with changes to specific developmental pathways and metazoan innovations. In particular, we discuss the origins of the recently described pharyngeal cluster which is conserved across deuterostome genomes, and highlight different genomic features that have contributed to the evolution of this group. We also assess our current capacity to infer ancestral metazoan states from gene models and comparative genomics tools and elaborate on the future directions of metazoan comparative genomics relevant to evo-devo studies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Multiple ancient origins of neoteny in Lycidae (Coleoptera): consequences for ecology and macroevolution

PubMed Central

Bocak, Ladislav; Bocakova, Milada; Hunt, Toby; Vogler, Alfried P

2008-01-01

Neoteny, the maintenance of larval features in sexually mature adults, is a radical way of generating evolutionary novelty through shifts in relative timing of developmental programmes. While controlled by the environment in facultative neotenics, retention of larval features is obligatory in many species of Lycidae (net-winged beetles). They are studied here as an example of how developmental shifts and ecology interact to produce macroevolutionary impacts. We conducted a phylogenetic analysis of Lycidae based on DNA sequences from nuclear (18S and 28S rRNA) and mitochondrial (rrnL, cox1, cob and nad5) genes from a representative set of lineages (73 species), including 17 neotenic taxa. Major changes of basal relationships compared with those implied in the current classification generally supported three independent origins of neotenics in Lycidae. The southeast Asian Lyropaeinae and Ateliinae were in basal positions indicating evolutionary antiquity, also confirmed by molecular clock estimates, unlike the neotropical leptolycines nested within Calopterini and presumably much younger. neotenics exhibit typical K-selected traits including slow development, large body size, high investment in offspring and low dispersal. This correlated with low species richness and restricted ranges of neotenic lineages compared with their sisters. Yet, these factors did not impede the evolutionary persistence of affected lineages, even without reversals to fully metamorphosed forms, contradicting earlier suggestions of recent evolution from dispersive non-neotenics. PMID:18477542

Neutral Evolution of Duplicated DNA: An Evolutionary Stick-Breaking Process Causes Scale-Invariant Behavior

NASA Astrophysics Data System (ADS)

Massip, Florian; Arndt, Peter F.

2013-04-01

Recently, an enrichment of identical matching sequences has been found in many eukaryotic genomes. Their length distribution exhibits a power law tail raising the question of what evolutionary mechanism or functional constraints would be able to shape this distribution. Here we introduce a simple and evolutionarily neutral model, which involves only point mutations and segmental duplications, and produces the same statistical features as observed for genomic data. Further, we extend a mathematical model for random stick breaking to analytically show that the exponent of the power law tail is -3 and universal as it does not depend on the microscopic details of the model.

Feeling of Certainty: Uncovering a Missing Link between Knowledge and Acceptance of Evolution

ERIC Educational Resources Information Center

Ha, Minsu; Haury, David L.; Nehm, Ross H.

2012-01-01

We propose a new model of the factors influencing acceptance of evolutionary theory that highlights a novel variable unexplored in previous studies: the feeling of certainty (FOC). The model is grounded in an emerging understanding of brain function that acknowledges the contributions of intuitive cognitions in making decisions, such as whether or…

It's time to Rework the Blueprints: Building a Science for Clinical Psychology

ERIC Educational Resources Information Center

Millon, Theodore

2003-01-01

The aims in this article are to connect the conceptual structure of clinical psychological science to what the author believes to be the omnipresent principles of evolution, use the evolutionary model to create a deductively derived clinical theory and taxonomy, link the theory and taxonomy to comprehensive and integrated approaches to assessment,…

Have Sex Differences in Spatial Ability Evolved from Male Competition for Mating and Female Concern for Survival?

ERIC Educational Resources Information Center

Ecuyer-Dab, Isabelle; Robert, Michele

2004-01-01

Drawing on the theoretical and empirical foundations of two evolutionary models, we argue that, among humans and other mammals, a twofold selection process would parsimoniously account for sex-linked advantages in spatial contexts. In males, a superiority for both solving navigation-related spatial problems and understanding physical principles…

RELATIONSHIP BETWEEN PHYLOGENETIC DISTRIBUTION AND GENOMIC FEATURES IN NEUROSPORA CRASSA

USDA-ARS?s Scientific Manuscript database

In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genome data. We demonstrate that an evolutionary approach, which is independent of functional annotation, has great potential as a tool for genome analysis. We chose the genome o...

Semantic Web Compatible Names and Descriptions for Organisms

NASA Astrophysics Data System (ADS)

Wang, H.; Wilson, N.; McGuinness, D. L.

2012-12-01

Modern scientific names are critical for understanding the biological literature and provide a valuable way to understand evolutionary relationships. To validly publish a name, a description is required to separate the described group of organisms from those described by other names at the same level of the taxonomic hierarchy. The frequent revision of descriptions due to new evolutionary evidence has lead to situations where a single given scientific name may over time have multiple descriptions associated with it and a given published description may apply to multiple scientific names. Because of these many-to-many relationships between scientific names and descriptions, the usage of scientific names as a proxy for descriptions is inevitably ambiguous. Another issue lies in the fact that the precise application of scientific names often requires careful microscopic work, or increasingly, genetic sequencing, as scientific names are focused on the evolutionary relatedness between and within named groups such as species, genera, families, etc. This is problematic to many audiences, especially field biologists, who often do not have access to the instruments and tools required to make identifications on a microscopic or genetic basis. To better connect scientific names to descriptions and find a more convenient way to support computer assisted identification, we proposed the Semantic Vernacular System, a novel naming system that creates named, machine-interpretable descriptions for groups of organisms, and is compatible with the Semantic Web. Unlike the evolutionary relationship based scientific naming system, it emphasizes the observable features of organisms. By independently naming the descriptions composed of sets of observational features, as well as maintaining connections to scientific names, it preserves the observational data used to identify organisms. The system is designed to support a peer-review mechanism for creating new names, and uses a controlled vocabulary encoded in the Web Ontology Language to represent the observational features. A prototype of the system is currently under development in collaboration with the Mushroom Observer website. It allows users to propose new names and descriptions for fungi, provide feedback on those proposals, and ultimately have them formally approved. It relies on SPARQL queries and semantic reasoning for data management. This effort will offer the mycology community a knowledge base of fungal observational features and a tool for identifying fungal observations. It will also serve as an operational specification of how the Semantic Vernacular System can be used in practice in one scientific community (in this case mycology).

Testing inferences in developmental evolution: the forensic evidence principle.

PubMed

Larsson, Hans C E; Wagner, Günter P

2012-09-01

Developmental evolution (DE) examines the influence of developmental mechanisms on biological evolution. Here we consider the question: "what is the evidence that allows us to decide whether a certain developmental scenario for an evolutionary change is in fact "correct" or at least falsifiable?" We argue that the comparative method linked with what we call the "forensic evidence principle" (FEP) is sufficient to conduct rigorous tests of DE scenarios. The FEP states that different genetically mediated developmental causes of an evolutionary transformation will leave different signatures in the development of the derived character. Although similar inference rules have been used in practically every empirical science, we expand this approach here in two ways: (1) we justify the validity of this principle with reference to a well-known result from mathematical physics, known as the symmetry principle, and (2) propose a specific form of the FEP for DE: given two or more developmental explanations for a certain evolutionary event, say an evolutionary novelty, then the evidence discriminating between these hypotheses will be found in the most proximal internal drivers of the derived character. Hence, a detailed description of the ancestral and derived states, and their most proximal developmental drivers are necessary to discriminate between various evolutionary developmental hypotheses. We discuss how this stepwise order of testing is necessary, establishes a formal test, and how skipping this order of examination may violate a more accurate examination of DE. We illustrate the approach with an example from avian digit evolution. © 2012 Wiley Periodicals, Inc.

Brain, calvarium, cladistics: A new approach to an old question, who are modern humans and Neandertals?

PubMed

Mounier, Aurélien; Balzeau, Antoine; Caparros, Miguel; Grimaud-Hervé, Dominique

2016-03-01

The evolutionary history of the genus Homo is the focus of major research efforts in palaeoanthropology. However, the use of palaeoneurology to infer phylogenies of our genus is rare. Here we use cladistics to test the importance of the brain in differentiating and defining Neandertals and modern humans. The analysis is based on morphological data from the calvarium and endocast of Pleistocene fossils and results in a single most parsimonious cladogram. We demonstrate that the joint use of endocranial and calvarial features with cladistics provides a unique means to understand the evolution of the genus Homo. The main results of this study indicate that: (i) the endocranial features are more phylogenetically informative than the characters from the calvarium; (ii) the specific differentiation of Neandertals and modern humans is mostly supported by well-known calvarial autapomorphies; (iii) the endocranial anatomy of modern humans and Neandertals show strong similarities, which appeared in the fossil record with the last common ancestor of both species; and (iv) apart from encephalisation, human endocranial anatomy changed tremendously during the end of the Middle Pleistocene. This may be linked to major cultural and technological novelties that had happened by the end of the Middle Pleistocene (e.g., expansion of the Middle Stone Age (MSA) in Africa and Mousterian in Europe). The combined study of endocranial and exocranial anatomy offers opportunities to further understand human evolution and the implication for the phylogeny of our genus. Copyright © 2015 Elsevier Ltd. All rights reserved.

Lack of sex chromosome specific meiotic silencing in platypus reveals origin of MSCI in therian mammals.

PubMed

Daish, Tasman J; Casey, Aaron E; Grutzner, Frank

2015-12-10

In therian mammals heteromorphic sex chromosomes are subject to meiotic sex chromosome inactivation (MSCI) during meiotic prophase I while the autosomes maintain transcriptional activity. The evolution of this sex chromosome silencing is thought to result in retroposition of genes required in spermatogenesis from the sex chromosomes to autosomes. In birds sex chromosome specific silencing appears to be absent and global transcriptional reductions occur through pachytene and sex chromosome-derived autosomal retrogenes are lacking. Egg laying monotremes are the most basal mammalian lineage, feature a complex and highly differentiated XY sex chromosome system with homology to the avian sex chromosomes, and also lack autosomal retrogenes. In order to delineate the point of origin of sex chromosome specific silencing in mammals we investigated whether MSCI exists in platypus. Our results show that platypus sex chromosomes display only partial or transient colocalisation with a repressive histone variant linked to therian sex chromosome silencing and surprisingly lack a hallmark MSCI epigenetic signature present in other mammals. Remarkably, platypus instead feature an avian like period of general low level transcription through prophase I with the sex chromosomes and the future mammalian X maintaining association with a nucleolus-like structure. Our work demonstrates for the first time that in mammals meiotic silencing of sex chromosomes evolved after the divergence of monotremes presumably as a result of the differentiation of the therian XY sex chromosomes. We provide a novel evolutionary scenario on how the future therian X chromosome commenced the trajectory toward MSCI.

Functional and evolutionary aspects of axial stability in euarchontans and other mammals.

PubMed

Granatosky, Michael C; Lemelin, Pierre; Chester, Stephen G B; Pampush, James D; Schmitt, Daniel

2014-03-01

The presence of a stable thoracolumbar region, found in many arboreal mammals, is considered advantageous for bridging and cantilevering between discontinuous branches. However, no study has directly explored the link between osteological features cited as enhancing axial stability and the frequency of cantilevering and bridging behaviors in a terminal branch environment. To fill this gap, we collected metric data on costal and vertebral morphology of primate and nonprimate mammals known to cantilever and bridge frequently and those that do not. We also quantified the frequency and duration of cantilevering and bridging behaviors using experimental setups for species that have been reported to show differences in use of small branches and back anatomy (Caluromys philander, Loris tardigradus, Monodelphis domestica, and Cheirogaleus medius). Phylogenetically corrected principal component analysis reveals that taxa employing frequent bridging and cantilevering (C. philander and lorises) also exhibit reduced intervertebral and intercostal spaces, which can serve to increase thoracolumbar stability, when compared to closely related species (M. domestica and C. medius). We observed C. philander cantilevering and bridging significantly more often than M. domestica, which never cantilevered or crossed any arboreal gaps. Although no difference in the frequency of cantilevering was observed between L. tardigradus and C. medius, the duration of cantilevering bouts was significantly greater in L. tardigradus. These data suggest that osteological features promoting axial rigidity may be part of a morpho-behavioral complex that increases stability in mammals moving and foraging in a terminal branch environment. Copyright © 2013 Wiley Periodicals, Inc.

An evolutionary computation based algorithm for calculating solar differential rotation by automatic tracking of coronal bright points

NASA Astrophysics Data System (ADS)

Shahamatnia, Ehsan; Dorotovič, Ivan; Fonseca, Jose M.; Ribeiro, Rita A.

2016-03-01

Developing specialized software tools is essential to support studies of solar activity evolution. With new space missions such as Solar Dynamics Observatory (SDO), solar images are being produced in unprecedented volumes. To capitalize on that huge data availability, the scientific community needs a new generation of software tools for automatic and efficient data processing. In this paper a prototype of a modular framework for solar feature detection, characterization, and tracking is presented. To develop an efficient system capable of automatic solar feature tracking and measuring, a hybrid approach combining specialized image processing, evolutionary optimization, and soft computing algorithms is being followed. The specialized hybrid algorithm for tracking solar features allows automatic feature tracking while gathering characterization details about the tracked features. The hybrid algorithm takes advantages of the snake model, a specialized image processing algorithm widely used in applications such as boundary delineation, image segmentation, and object tracking. Further, it exploits the flexibility and efficiency of Particle Swarm Optimization (PSO), a stochastic population based optimization algorithm. PSO has been used successfully in a wide range of applications including combinatorial optimization, control, clustering, robotics, scheduling, and image processing and video analysis applications. The proposed tool, denoted PSO-Snake model, was already successfully tested in other works for tracking sunspots and coronal bright points. In this work, we discuss the application of the PSO-Snake algorithm for calculating the sidereal rotational angular velocity of the solar corona. To validate the results we compare them with published manual results performed by an expert.

Evolutionary Ecology of Organs: A Missing Link in Cancer Development?

PubMed

Thomas, Frédéric; Nesse, Randolph M; Gatenby, Robert; Gidoin, Cindy; Renaud, François; Roche, Benjamin; Ujvari, Beata

2016-08-01

There is striking variation in the incidence of cancer in human organs. Malignant tumors are common in the colon and breast but rare in the heart and small bowel. The uterus frequently develops benign fibroid tumors but uterine cancers are relatively rare. The organ-specific difference in cancer prevalence has been explained primarily by the relative roles of intrinsic and extrinsic risk factors. In this opinion article, we propose also considering organs as distinct but connected ecosystems whose different vulnerabilities to malignant transformation may be partially explained by how essential each organ is for survival through the age of reproduction. We present and discuss some of the basic concepts and assumptions of this perspective on evolutionary medicine. Copyright © 2016 Elsevier Inc. All rights reserved.

An Evolutionary Cascade Model for Sauropod Dinosaur Gigantism - Overview, Update and Tests

PubMed Central

Sander, P. Martin

2013-01-01

Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades (“Reproduction”, “Feeding”, “Head and neck”, “Avian-style lung”, and “Metabolism”). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait “Very high body mass”. Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size. PMID:24205267

Connecting proximate mechanisms and evolutionary patterns: pituitary gland size and mammalian life history.

PubMed

Kamilar, J M; Tecot, S R

2015-11-01

At the proximate level, hormones are known to play a critical role in influencing the life history of mammals, including humans. The pituitary gland is directly responsible for producing several hormones, including those related to growth and reproduction. Although we have a basic understanding of how hormones affect life history characteristics, we still have little knowledge of this relationship in an evolutionary context. We used data from 129 mammal species representing 14 orders to investigate the relationship between pituitary gland size and life history variation. Because pituitary gland size should be related to hormone production and action, we predicted that species with relatively large pituitaries should be associated with fast life histories, especially increased foetal and post-natal growth rates. Phylogenetic analyses revealed that total pituitary size and the size of the anterior lobe of the pituitary significantly predicted a life history axis that was correlated with several traits including body mass, and foetal and post-natal growth rates. Additional models directly examining the association between relative pituitary size and growth rates produced concordant results. We also found that relative pituitary size variation across mammals was best explained by an Ornstein-Uhlenbeck model of evolution, suggesting an important role of stabilizing selection. Our results support the idea that the size of the pituitary is linked to life history variation through evolutionary time. This pattern is likely due to mediating hormone levels but additional work is needed. We suggest that future investigations incorporating endocrine gland size may be critical for understanding life history evolution. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

An evolutionary cascade model for sauropod dinosaur gigantism--overview, update and tests.

PubMed

Sander, P Martin

2013-01-01

Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades ("Reproduction", "Feeding", "Head and neck", "Avian-style lung", and "Metabolism"). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait "Very high body mass". Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size.

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical Society of America.

Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks

PubMed Central

Robinson, Kathryn M; Hauzy, Céline; Loeuille, Nicolas; Albrectsen, Benedicte R

2015-01-01

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint. PMID:26306175

The tale of the shrinking weapon: seasonal changes in nutrition affect weapon size and sexual dimorphism, but not contemporary evolution.

PubMed

Miller, C W; McDonald, G C; Moore, A J

2016-11-01

Sexually selected traits are often highly variable in size within populations due to their close link with the physical condition of individuals. Nutrition has a large impact on physical condition, and thus, any seasonal changes in nutritional quality are predicted to alter the average size of sexually selected traits as well as the degree of sexual dimorphism in populations. However, although traits affected by mate choice are well studied, we have a surprising lack of knowledge of how natural variation in nutrition affects the expression of sexually selected weapons and sexual dimorphism. Further, few studies explicitly test for differences in the heritability and mean-scaled evolvability of sexually selected traits across conditions. We studied Narnia femorata (Hemiptera: Coreidae), an insect where males use their hind legs as weapons and the femurs are enlarged, to understand the extent to which weapon expression, sexual dimorphism and evolvability change across the actual range of nutrition available in the wild. We found that insects raised on a poor diet (cactus without fruit) are nearly monomorphic, whereas those raised on a high-quality diet (cactus with ripe fruit) are distinctly sexually dimorphic via the expression of large hind leg weapons in males. Contrary to our expectations, we found little evidence of a potential for evolutionary change for any trait measured. Thus, although we show weapons are highly condition dependent, and changes in weapon expression and dimorphism could alter evolutionary dynamics, our populations are unlikely to experience further evolutionary changes under current conditions. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Linking micro- and macro-evolution at the cell type level: a view from the lophotrochozoan Platynereis dumerilii.

PubMed

Simakov, Oleg; Larsson, Tomas A; Arendt, Detlev

2013-09-01

Ever since the origin of the first metazoans over 600 million years ago, cell type diversification has been driven by micro-evolutionary processes at population level, leading to macro-evolution changes above species level. In this review, we introduce the marine annelid Platynereis dumerilii, a member of the lophotrochozoan clade (a key yet most understudied superphylum of bilaterians), as a suitable model system for the simultaneous study, at cellular resolution, of macro-evolutionary processes across phyla and of micro-evolutionary processes across highly polymorphic populations collected worldwide. Recent advances in molecular and experimental techniques, easy maintenance and breeding, and the fast, synchronous and stereotypical development have facilitated the establishment of Platynereis as one of the leading model species in the eco-evo-devo field. Most importantly, Platynereis allows the combination of expression profiling, morphological and physiological characterization at the single cell level. Here, we discuss recent advances in the collection of -omics data for the lab strain and for natural populations collected world-wide that can be integrated with population-specific cellular analyses to result in a cellular atlas integrating genetic, phenotypic and ecological variation. This makes Platynereis a tractable system to begin understanding the interplay between macro- and micro-evolutionary processes and cell type diversity.

Evolution in biodiversity policy – current gaps and future needs

PubMed Central

Santamaría, Luis; Méndez, Pablo F

2012-01-01

The intensity and speed of human alterations to the planet's ecosystems are yielding our static, ahistorical view of biodiversity obsolete. Human actions frequently trigger fast evolutionary responses, affect extant genetic variation and result in the establishment of new communities and co-evolutionary networks for which we lack past analogues. Contemporary evolution interplays with ecological changes to determine the response of organisms and ecosystems to anthropogenic pressures. Examples on wild species include responses to harvest (e.g. fisheries, hunting, angling), habitat loss and fragmentation (e.g. genetic effects of isolation), biotic exchange (e.g. evolutionary responses to control measures), climate change (e.g. local adaptation and its interplay with dispersal processes) and the responses of endangered species to conservation measures. A review of international and EU biodiversity policies showed numerous opportunities for the integration of evolutionary knowledge, with the realistic prospect of improving their efficacy. Such opportunities should be extended to other sectoral policies of direct relevance for biodiversity – notably nature conservation, fisheries, agriculture, water resources, spatial planning and climate change. These avenues for improvement are, however, challenged by the low level of enforcement of biodiversity policies, linked to the nonbinding nature of most biodiversity-policy documents, and the decreasing representation of biodiversity in EU's research policy. PMID:25568042

Evolutionary relationships of flying foxes (genus Pteropus) in the Philippines inferred from DNA sequences of cytochrome b gene.

PubMed

Bastian, S T; Tanaka, K; Anunciado, R V P; Natural, N G; Sumalde, A C; Namikawa, T

2002-04-01

Six flying fox species, genus Pteropus (four from the Philippines) were investigated using complete cytochrome b gene sequences (1140 bp) to infer their evolutionary relationships. The DNA sequences generated via polymerase chain reaction were analyzed using the neighbor-joining, parsimony, and maximum likelihood methods. We estimated that the first evolutionary event among these Pteropus species occurred approximately 13.90 +/- 1.49 MYA. Within this short period of evolutionary time we further hypothesized that the ancestors of the flying foxes found in the Philippines experienced a subsequent diversification forming two clusters in the topology. The first cluster is composed of P. pumilus (Philippine endemic), P. speciosus (restricted in western Mindanao) with P. scapulatus, while the second one comprised P. vampyrus and P. dasymallus species based on the analysis from first and second codon positions. Consistently, all phylogenetic analyses divulged close association of P. dasymallus with P. vampyrus contradicting the previous report categorizing P. dasymallus under subniger species group with P. pumilus. P. speciosus, and P. hypomelanus. The Philippine endemic species (P. pumilus) is closely linked with P. speciosus. The representative samples of P. vampyrus showed a large genetic distance of 1.87%. The large genetic distance between P. dasymallus and P. hypomelanus, P. pumilus and P. speciosus denotes a distinct species group.

Spatial Selection and Local Adaptation Jointly Shape Life-History Evolution during Range Expansion.

PubMed

Van Petegem, Katrien H P; Boeye, Jeroen; Stoks, Robby; Bonte, Dries

2016-11-01

In the context of climate change and species invasions, range shifts increasingly gain attention because the rates at which they occur in the Anthropocene induce rapid changes in biological assemblages. During range shifts, species experience multiple selection pressures. For poleward expansions in particular, it is difficult to interpret observed evolutionary dynamics because of the joint action of evolutionary processes related to spatial selection and to adaptation toward local climatic conditions. To disentangle the effects of these two processes, we integrated stochastic modeling and data from a common garden experiment, using the spider mite Tetranychus urticae as a model species. By linking the empirical data with those derived form a highly parameterized individual-based model, we infer that both spatial selection and local adaptation contributed to the observed latitudinal life-history divergence. Spatial selection best described variation in dispersal behavior, while variation in development was best explained by adaptation to the local climate. Divergence in life-history traits in species shifting poleward could consequently be jointly determined by contemporary evolutionary dynamics resulting from adaptation to the environmental gradient and from spatial selection. The integration of modeling with common garden experiments provides a powerful tool to study the contribution of these evolutionary processes on life-history evolution during range expansion.

Population differentiation in the context of Holocene climate change for a migratory marine species, the southern elephant seal.

PubMed

Corrigan, L J; Fabiani, A; Chauke, L F; McMahon, C R; de Bruyn, M; Bester, M N; Bastos, A; Campagna, C; Muelbert, M M C; Hoelzel, A R

2016-09-01

Understanding observed patterns of connectivity requires an understanding of the evolutionary processes that determine genetic structure among populations, with the most common models being associated with isolation by distance, allopatry or vicariance. Pinnipeds are annual breeders with the capacity for extensive range overlap during seasonal migrations, establishing the potential for the evolution of isolation by distance. Here, we assess the pattern of differentiation among six breeding colonies of the southern elephant seal, Mirounga leonina, based on mtDNA and 15 neutral microsatellite DNA markers, and consider measures of their demography and connectivity. We show that all breeding colonies are genetically divergent and that connectivity in this highly mobile pinniped is not strongly associated with geographic distance, but more likely linked to Holocene climate change and demographic processes. Estimates of divergence times between populations were all after the last glacial maximum, and there was evidence for directional migration in a clockwise pattern (with the prevailing current) around the Antarctic. We discuss the mechanisms by which climate change may have contributed to the contemporary genetic structure of southern elephant seal populations and the broader implications. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Does sex speed up evolutionary rate and increase biodiversity?

PubMed

Melián, Carlos J; Alonso, David; Allesina, Stefano; Condit, Richard S; Etienne, Rampal S

2012-01-01

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.

Biological and geophysical feedbacks with fire in the Earth system

NASA Astrophysics Data System (ADS)

Archibald, S.; Lehmann, C. E. R.; Belcher, C. M.; Bond, W. J.; Bradstock, R. A.; Daniau, A.-L.; Dexter, K. G.; Forrestel, E. J.; Greve, M.; He, T.; Higgins, S. I.; Hoffmann, W. A.; Lamont, B. B.; McGlinn, D. J.; Moncrieff, G. R.; Osborne, C. P.; Pausas, J. G.; Price, O.; Ripley, B. S.; Rogers, B. M.; Schwilk, D. W.; Simon, M. F.; Turetsky, M. R.; Van der Werf, G. R.; Zanne, A. E.

2018-03-01

Roughly 3% of the Earth’s land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences.

Evolution of heliobacteria: implications for photosynthetic reaction center complexes

NASA Technical Reports Server (NTRS)

Vermaas, W. F.; Blankenship, R. E. (Principal Investigator)

1994-01-01

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein show rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to the core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

PubMed

Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D

2017-10-01

Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.

Conciliation biology: the eco-evolutionary management of permanently invaded biotic systems

PubMed Central

Carroll, Scott P

2011-01-01

Biotic invaders and similar anthropogenic novelties such as domesticates, transgenics, and cancers can alter ecology and evolution in environmental, agricultural, natural resource, public health, and medical systems. The resulting biological changes may either hinder or serve management objectives. For example, biological control and eradication programs are often defeated by unanticipated resistance evolution and by irreversibility of invader impacts. Moreover, eradication may be ill-advised when nonnatives introduce beneficial functions. Thus, contexts that appear to call for eradication may instead demand managed coexistence of natives with nonnatives, and yet applied biologists have not generally considered the need to manage the eco-evolutionary dynamics that commonly result from interactions of natives with nonnatives. Here, I advocate a conciliatory approach to managing systems where novel organisms cannot or should not be eradicated. Conciliatory strategies incorporate benefits of nonnatives to address many practical needs including slowing rates of resistance evolution, promoting evolution of indigenous biological control, cultivating replacement services and novel functions, and managing native–nonnative coevolution. Evolutionary links across disciplines foster cohesion essential for managing the broad impacts of novel biotic systems. Rather than signaling defeat, conciliation biology thus utilizes the predictive power of evolutionary theory to offer diverse and flexible pathways to more sustainable outcomes. PMID:25567967

Wood anatomical correlates with theoretical conductivity and wood density across China: evolutionary evidence of the functional differentiation of axial and radial parenchyma

PubMed Central

Zheng, Jingming; Martínez-Cabrera, Hugo I.

2013-01-01

Background and Aims In recent years considerable effort has focused on linking wood anatomy and key ecological traits. Studies analysing large databases have described how these ecological traits vary as a function of wood anatomical traits related to conduction and support, but have not considered how these functions interact with cells involved in storage of water and carbohydrates (i.e. parenchyma cells). Methods We analyzed, in a phylogenetic context, the functional relationship between cell types performing each of the three xylem functions (conduction, support and storage) and wood density and theoretical conductivity using a sample of approx. 800 tree species from China. Key Results Axial parenchyma and rays had distinct evolutionary correlation patterns. An evolutionary link was found between high conduction capacity and larger amounts of axial parenchyma that is probably related to water storage capacity and embolism repair, while larger amounts of ray tissue have evolved with increased mechanical support and reduced hydraulic capacity. In a phylogenetic principal component analysis this association of axial parenchyma with increased conduction capacity and rays with wood density represented orthogonal axes of variation. In multivariate space, however, the proportion of rays might be positively associated with conductance and negatively with wood density, indicating flexibility in these axes in species with wide rays. Conclusions The findings suggest that parenchyma types may differ in function. The functional axes represented by different cell types were conserved across lineages, suggesting a significant role in the ecological strategies of the angiosperms. PMID:23904446

δ-Conotoxin SuVIA suggests an evolutionary link between ancestral predator defence and the origin of fish-hunting behaviour in carnivorous cone snails.

PubMed

Jin, Ai-Hua; Israel, Mathilde R; Inserra, Marco C; Smith, Jennifer J; Lewis, Richard J; Alewood, Paul F; Vetter, Irina; Dutertre, Sébastien

2015-07-22

Some venomous cone snails feed on small fishes using an immobilizing combination of synergistic venom peptides that target Kv and Nav channels. As part of this envenomation strategy, δ-conotoxins are potent ichtyotoxins that enhance Nav channel function. δ-Conotoxins belong to an ancient and widely distributed gene superfamily, but any evolutionary link from ancestral worm-eating cone snails to modern piscivorous species has not been elucidated. Here, we report the discovery of SuVIA, a potent vertebrate-active δ-conotoxin characterized from a vermivorous cone snail (Conus suturatus). SuVIA is equipotent at hNaV1.3, hNaV1.4 and hNaV1.6 with EC50s in the low nanomolar range. SuVIA also increased peak hNaV1.7 current by approximately 75% and shifted the voltage-dependence of activation to more hyperpolarized potentials from -15 mV to -25 mV, with little effect on the voltage-dependence of inactivation. Interestingly, the proximal venom gland expression and pain-inducing effect of SuVIA in mammals suggest that δ-conotoxins in vermivorous cone snails play a defensive role against higher order vertebrates. We propose that δ-conotoxins originally evolved in ancestral vermivorous cones to defend against larger predators including fishes have been repurposed to facilitate a shift to piscivorous behaviour, suggesting an unexpected underlying mechanism for this remarkable evolutionary transition. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches.

PubMed

Siver, Peter A; Jo, Bok Yeon; Kim, Jong Im; Shin, Woongghi; Lott, Anne Marie; Wolfe, Alexander P

2015-06-01

Heterokont algae of the class Synurophyceae, characterized by distinctive siliceous scales that cover the surface of the cell, are ecologically important in inland waters, yet their evolutionary history remains enigmatic. We explore phylogenetic relationships within this group of algae relative to geologic time, with a focus on evolution of siliceous components. We combined an expansive five-gene and time-calibrated molecular phylogeny of synurophyte algae with an extensive array of fossil specimens from the middle Eocene to infer evolutionary trends within the group. The group originated in the Jurassic approximately 157 million years ago (Ma), with the keystone genera Mallomonas and Synura diverging during the Early Cretaceous at 130 Ma. Mallomonas further splits into two major subclades, signaling the evolution of the V-rib believed to aid in the spacing and organization of scales on the cell covering. Synura also diverges into two primary subclades, separating taxa with forward-projecting spines on the scale from those with a keel positioned on the scale proper. Approximately one third of the fossil species are extinct, whereas the remaining taxa are linked to modern congeners. The taxonomy of synurophytes, which relies extensively on the morphology of the siliceous components, is largely congruent with molecular analyses. Scales of extinct synurophytes were significantly larger than those of modern taxa and may have played a role in their demise. In contrast, many fossil species linked to modern lineages were smaller in the middle Eocene, possibly reflecting growth in the greenhouse climatic state that characterized this geologic interval. © 2015 Botanical Society of America, Inc.

Evolutionary dynamics of a smoothed war of attrition game.

PubMed

Iyer, Swami; Killingback, Timothy

2016-05-07

In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Architecture of an Antagonistic Tree/Fungus Network: The Asymmetric Influence of Past Evolutionary History

PubMed Central

Vacher, Corinne; Piou, Dominique; Desprez-Loustau, Marie-Laure

2008-01-01

Background Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Methology/Principal Findings Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Conclusion/Significance Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes. PMID:18320058

Gender approaches to evolutionary multi-objective optimization using pre-selection of criteria

NASA Astrophysics Data System (ADS)

Kowalczuk, Zdzisław; Białaszewski, Tomasz

2018-01-01

A novel idea to perform evolutionary computations (ECs) for solving highly dimensional multi-objective optimization (MOO) problems is proposed. Following the general idea of evolution, it is proposed that information about gender is used to distinguish between various groups of objectives and identify the (aggregate) nature of optimality of individuals (solutions). This identification is drawn out of the fitness of individuals and applied during parental crossover in the processes of evolutionary multi-objective optimization (EMOO). The article introduces the principles of the genetic-gender approach (GGA) and virtual gender approach (VGA), which are not just evolutionary techniques, but constitute a completely new rule (philosophy) for use in solving MOO tasks. The proposed approaches are validated against principal representatives of the EMOO algorithms of the state of the art in solving benchmark problems in the light of recognized EC performance criteria. The research shows the superiority of the gender approach in terms of effectiveness, reliability, transparency, intelligibility and MOO problem simplification, resulting in the great usefulness and practicability of GGA and VGA. Moreover, an important feature of GGA and VGA is that they alleviate the 'curse' of dimensionality typical of many engineering designs.

Mode and tempo in the evolution of socio-political organization: reconciling 'Darwinian' and 'Spencerian' evolutionary approaches in anthropology.

PubMed

Currie, Thomas E; Mace, Ruth

2011-04-12

Traditional investigations of the evolution of human social and political institutions trace their ancestry back to nineteenth century social scientists such as Herbert Spencer, and have concentrated on the increase in socio-political complexity over time. More recent studies of cultural evolution have been explicitly informed by Darwinian evolutionary theory and focus on the transmission of cultural traits between individuals. These two approaches to investigating cultural change are often seen as incompatible. However, we argue that many of the defining features and assumptions of 'Spencerian' cultural evolutionary theory represent testable hypotheses that can and should be tackled within a broader 'Darwinian' framework. In this paper we apply phylogenetic comparative techniques to data from Austronesian-speaking societies of Island South-East Asia and the Pacific to test hypotheses about the mode and tempo of human socio-political evolution. We find support for three ideas often associated with Spencerian cultural evolutionary theory: (i) political organization has evolved through a regular sequence of forms, (ii) increases in hierarchical political complexity have been more common than decreases, and (iii) political organization has co-evolved with the wider presence of hereditary social stratification.

An evolutionary ecology of individual differences

PubMed Central

Dall, Sasha R. X.; Bell, Alison M.; Bolnick, Daniel I.; Ratnieks, Francis L. W.

2014-01-01

Individuals often differ in what they do. This has been recognised since antiquity. Nevertheless, the ecological and evolutionary significance of such variation is attracting widespread interest, which is burgeoning to an extent that is fragmenting the literature. As a first attempt at synthesis, we focus on individual differences in behaviour within populations that exceed the day-to-day variation in individual behaviour (i.e. behavioural specialisation). Indeed, the factors promoting ecologically relevant behavioural specialisation within natural populations are likely to have far-reaching ecological and evolutionary consequences. We discuss such individual differences from three distinct perspectives: individual niche specialisations, the division of labour within insect societies and animal personality variation. In the process, while recognising that each area has its own unique motivations, we identify a number of opportunities for productive ‘crossfertilisation’ among the (largely independent) bodies of work. We conclude that a complete understanding of evolutionarily and ecologically relevant individual differences must specify how ecological interactions impact the basic biological process (e.g. Darwinian selection, development and information processing) that underpin the organismal features determining behavioural specialisations. Moreover, there is likely to be covariation amongst behavioural specialisations. Thus, we sketch the key elements of a general framework for studying the evolutionary ecology of individual differences. PMID:22897772

Mode and tempo in the evolution of socio-political organization: reconciling ‘Darwinian’ and ‘Spencerian’ evolutionary approaches in anthropology

PubMed Central

Currie, Thomas E.; Mace, Ruth

2011-01-01

Traditional investigations of the evolution of human social and political institutions trace their ancestry back to nineteenth century social scientists such as Herbert Spencer, and have concentrated on the increase in socio-political complexity over time. More recent studies of cultural evolution have been explicitly informed by Darwinian evolutionary theory and focus on the transmission of cultural traits between individuals. These two approaches to investigating cultural change are often seen as incompatible. However, we argue that many of the defining features and assumptions of ‘Spencerian’ cultural evolutionary theory represent testable hypotheses that can and should be tackled within a broader ‘Darwinian’ framework. In this paper we apply phylogenetic comparative techniques to data from Austronesian-speaking societies of Island South-East Asia and the Pacific to test hypotheses about the mode and tempo of human socio-political evolution. We find support for three ideas often associated with Spencerian cultural evolutionary theory: (i) political organization has evolved through a regular sequence of forms, (ii) increases in hierarchical political complexity have been more common than decreases, and (iii) political organization has co-evolved with the wider presence of hereditary social stratification. PMID:21357233

[Narcissism in the world of Facebook. An evolutionary psychopathological interpretation].

PubMed

Szekeres, Adám; Tisljár, Roland

2013-01-01

In the last few decades there has been a considerable increase in the levels of narcissism among the population of individualistic, western cultures. The phenomena of narcissism induced a large number of psychological researches, some of which approaches the issue from changes in environmental factors. The modern environment of these days is substantially different from the one to which our ancestors have adapted over millions of years of evolution. The research results of narcissism from the perspective of evolutionary psychopathology approach have yet to integrate.The present review focuses on two studies and empirical findings induced by them in which an attempt is made to explore the evolutionary origins of narcissism. Relating to these studies we present the main mechanisms by which evolution may have played a role in the development and maintenance of narcissism. One of the significant elements of the current, changing social environment allowing virtual contacts is the social networking site called Facebook. Following the presentation of the main features of the site we discuss research results in connection with narcissistic traits and Facebook usage. Finally an attempt is made to integrate these findings into an evolutionary psychopathological framework.

The Memories of NK Cells: Innate-Adaptive Immune Intrinsic Crosstalk

PubMed Central

Ortolani, Claudio; del Zotto, Genny; Luchetti, Francesca; Canonico, Barbara; Artico, Marco; Papa, Stefano

2016-01-01

Although NK cells are considered part of the innate immune system, a series of evidences has demonstrated that they possess characteristics typical of the adaptive immune system. These NK adaptive features, in particular their memory-like functions, are discussed from an ontogenetic and evolutionary point of view. PMID:28078307

The Memories of NK Cells: Innate-Adaptive Immune Intrinsic Crosstalk.

PubMed

Gabrielli, Sara; Ortolani, Claudio; Del Zotto, Genny; Luchetti, Francesca; Canonico, Barbara; Buccella, Flavia; Artico, Marco; Papa, Stefano; Zamai, Loris

2016-01-01

Although NK cells are considered part of the innate immune system, a series of evidences has demonstrated that they possess characteristics typical of the adaptive immune system. These NK adaptive features, in particular their memory-like functions, are discussed from an ontogenetic and evolutionary point of view.

An Evolutionary Machine Learning Framework for Big Data Sequence Mining

ERIC Educational Resources Information Center

Kamath, Uday Krishna

2014-01-01

Sequence classification is an important problem in many real-world applications. Unlike other machine learning data, there are no "explicit" features or signals in sequence data that can help traditional machine learning algorithms learn and predict from the data. Sequence data exhibits inter-relationships in the elements that are…

A Cretaceous eutriconodont and integument evolution in early mammals.

PubMed

Martin, Thomas; Marugán-Lobón, Jesús; Vullo, Romain; Martín-Abad, Hugo; Luo, Zhe-Xi; Buscalioni, Angela D

2015-10-15

The Mesozoic era (252-66 million years ago), known as the domain of dinosaurs, witnessed a remarkable ecomorphological diversity of early mammals. The key mammalian characteristics originated during this period and were prerequisite for their evolutionary success after extinction of the non-avian dinosaurs 66 million years ago. Many ecomorphotypes familiar to modern mammal fauna evolved independently early in mammalian evolutionary history. Here we report a 125-million-year-old eutriconodontan mammal from Spain with extraordinary preservation of skin and pelage that extends the record of key mammalian integumentary features into the Mesozoic era. The new mammalian specimen exhibits such typical mammalian features as pelage, mane, pinna, and a variety of skin structures: keratinous dermal scutes, protospines composed of hair-like tubules, and compound follicles with primary and secondary hairs. The skin structures of this new Mesozoic mammal encompass the same combination of integumentary features as those evolved independently in other crown Mammalia, with similarly broad structural variations as in extant mammals. Soft tissues in the thorax and abdomen (alveolar lungs and liver) suggest the presence of a muscular diaphragm. The eutriconodont has molariform tooth replacement, ossified Meckel's cartilage of the middle ear, and specialized xenarthrous articulations of posterior dorsal vertebrae, convergent with extant xenarthran mammals, which strengthened the vertebral column for locomotion.

Evolutionary and developmental implications of asymmetric brain folding in a large primate pedigree

PubMed Central

Atkinson, Elizabeth G.; Rogers, Jeffrey; Cheverud, James M.

2016-01-01

Bilateral symmetry is a fundamental property of the vertebrate central nervous system. Local deviations from symmetry provide various types of information about the development, evolution and function of elements within the CNS, especially the cerebral hemispheres. Here, we quantify the pattern and extent of asymmetry in cortical folding within the cerebrum of Papio baboons and assess the evolutionary and developmental implications of the findings. Analyses of directional asymmetry show a population-level trend in length measurements indicating that baboons are genetically predisposed to be asymmetrical, with the right side longer than the left in the anterior cerebrum while the left side is longer than the right posteriorly. We also find a corresponding bias to display a right frontal petalia (overgrowth of the anterior pole of the cerebral cortex on the right side). By quantifying fluctuating asymmetry, we assess canalization of brain features and the susceptibility of the baboon brain to developmental perturbations. We find that features are differentially canalized depending on their ontogenetic timing. We further deduce that development of the two hemispheres is to some degree independent. This independence has important implications for the evolution of cerebral hemispheres and their separate specialization. Asymmetry is a major feature of primate brains and is characteristic of both brain structure and function. PMID:26813679

JCE Feature Columns

NASA Astrophysics Data System (ADS)

Holmes, Jon L.

1999-05-01

The Features area of JCE Online is now readily accessible through a single click from our home page. In the Features area each column is linked to its own home page. These column home pages also have links to them from the online Journal Table of Contents pages or from any article published as part of that feature column. Using these links you can easily find abstracts of additional articles that are related by topic. Of course, JCE Online+ subscribers are then just one click away from the entire article. Finding related articles is easy because each feature column "site" contains links to the online abstracts of all the articles that have appeared in the column. In addition, you can find the mission statement for the column and the email link to the column editor that I mentioned above. At the discretion of its editor, a feature column site may contain additional resources. As an example, the Chemical Information Instructor column edited by Arleen Somerville will have a periodically updated bibliography of resources for teaching and using chemical information. Due to the increase in the number of these resources available on the WWW, it only makes sense to publish this information online so that you can get to these resources with a simple click of the mouse. We expect that there will soon be additional information and resources at several other feature column sites. Following in the footsteps of the Chemical Information Instructor, up-to-date bibliographies and links to related online resources can be made available. We hope to extend the online component of our feature columns with moderated online discussion forums. If you have a suggestion for an online resource you would like to see included, let the feature editor or JCE Online (jceonline@chem.wisc.edu) know about it. JCE Internet Features JCE Internet also has several feature columns: Chemical Education Resource Shelf, Conceptual Questions and Challenge Problems, Equipment Buyers Guide, Hal's Picks, Mathcad in the Chemistry Curriculum, and WWW Site Review. These columns differ from the print feature columns in that they use the Internet as the publication medium. Doing so allows these features to include continually updated information, digital components, and links to other online resources. The Conceptual Questions and Challenge Problems feature of JCE Internet serves as a good example for the kinds of resources that you can expect to find in an online feature column. Like other columns it contains a mission statement that defines the role of the column. It includes a digital library of continually updated examples of conceptual questions and challenge problems. (As I write this we have just added several new questions to the library.) It also includes a list of links to related online resources, information for authors about how to write questions and problems, and information for teachers about how to use conceptual questions and challenge problems. Teaching with Technology home page at JCE Online. One-Stop Feature Shop The updated Feature area of JCE Online offers information about all JCE feature columns in one place. It gives you a quick and convenient way to access a group of articles in a particular subject area. It provides authors and readers with a good definition of the column and its mission. It complements the print feature columns with online resources. It provides up-to-date bibliographies for selected areas of interest. And last, but not least, it provides that email address you can use to send that message of appreciation to the feature editor for his or her contribution to JCE and the chemical education community.

Modeling of the ground-to-SSFMB link networking features using SPW

NASA Technical Reports Server (NTRS)

Watson, John C.

1993-01-01

This report describes the modeling and simulation of the networking features of the ground-to-Space Station Freedom manned base (SSFMB) link using COMDISCO signal processing work-system (SPW). The networking features modeled include the implementation of Consultative Committee for Space Data Systems (CCSDS) protocols in the multiplexing of digitized audio and core data into virtual channel data units (VCDU's) in the control center complex and the demultiplexing of VCDU's in the onboard baseband signal processor. The emphasis of this work has been placed on techniques for modeling the CCSDS networking features using SPW. The objectives for developing the SPW models are to test the suitability of SPW for modeling networking features and to develop SPW simulation models of the control center complex and space station baseband signal processor for use in end-to-end testing of the ground-to-SSFMB S-band single access forward (SSAF) link.

Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

NASA Technical Reports Server (NTRS)

Hinman, Veronica F.; Nguyen, Albert T.; Cameron, R. Andrew; Davidson, Eric H.

2003-01-01

Evolutionary change in morphological features must depend on architectural reorganization of developmental gene regulatory networks (GRNs), just as true conservation of morphological features must imply retention of ancestral developmental GRN features. Key elements of the provisional GRN for embryonic endomesoderm development in the sea urchin are here compared with those operating in embryos of a distantly related echinoderm, a starfish. These animals diverged from their common ancestor 520-480 million years ago. Their endomesodermal fate maps are similar, except that sea urchins generate a skeletogenic cell lineage that produces a prominent skeleton lacking entirely in starfish larvae. A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated. A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages. The significance of this retention is highlighted by the observation of numerous specific differences in the GRN connections as well. A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo. Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered.

Potential responses to climate change in organisms with complex life histories: evolution and plasticity in Pacific salmon

Treesearch

L.G. Crozier; A.P. Hendry; P.W. Lawson; T.P. Quinn; N.J. Mantua; J. Battin; R.G. Shaw; R.B. Huey

2008-01-01

Salmon life histories are finely tuned to local environmental conditions, which are intimately linked to climate. We summarize the likely impacts of climate change on the physical environment of salmon in the Pacific Northwest and discuss the potential evolutionary consequences of these changes, with particular reference to Columbia River Basin spring/summer Chinook (...

Gender Differences in the Developmental Cascade from Harsh Parenting to Educational Attainment: An Evolutionary Perspective

ERIC Educational Resources Information Center

Hentges, Rochelle F.; Wang, Ming-Te

2018-01-01

This study utilized life history theory to test a developmental cascade model linking harsh parenting to low educational attainment. Multigroup models were examined to test for potential gender differences. The sample consisted of 1,482 adolescents followed up for 9 years starting in seventh grade (M[subscript age] = 12.74). Results supported…

Charles Darwin: His Life, Journeys and Discoveries. A Teacher's Guide.

ERIC Educational Resources Information Center

Overy, Caroline

This handbook aims to: (1) introduce teachers and pupils to Charles Darwin, his life and work at Down House, his voyage on the Beagle, and his evolutionary theory; (2) set his ideas within the wider context of the 19th century; (3) link the subject areas to the British National Curriculum, particularly in history, science, and English at various…

Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats

PubMed Central

Teske, Peter R.; Beheregaray, Luciano B.

2009-01-01

Seahorses (Syngnathidae: Hippocampus) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses’ upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species. PMID:19451164

Primary Emotional Systems and Personality: An Evolutionary Perspective

PubMed Central

Montag, Christian; Panksepp, Jaak

2017-01-01

The present article highlights important concepts of personality including stability issues from the perspective of situational demands and stability over the life-course. Following this more introductory section, we argue why individual differences in primary emotional systems may represent the phylogenetically oldest parts of human personality. Our argumentation leads to the need to increasingly consider individual differences in the raw affects/emotions of people to understand human personality in a bottom–up fashion, which can be coordinated with top–down perspectives. In support of this idea, we also review existing evidence linking individual differences in primal emotions as assessed with the Affective Neuroscience Personality Scales and the widely accepted Big Five Model of Personality. In this context, we provide additional evidence on the link between primal emotions and personality in German and Chinese sample populations. In short, this article addresses evolutionary perspectives in the evaluation of human personality, highlighting some of the ancestral emotional urges that probably still control variations in the construction of human personality structures. Moreover, we address how individual differences in primary emotional systems can illuminate linkages to major human psychopathologies and the potential advantages and disadvantages of carrying a certain personality trait within certain cultural/environmental niches. PMID:28443039

Rapid Y degeneration and dosage compensation in plant sex chromosomes

PubMed Central

Papadopulos, Alexander S. T.; Chester, Michael; Ridout, Kate; Filatov, Dmitry A.

2015-01-01

The nonrecombining regions of animal Y chromosomes are known to undergo genetic degeneration, but previous work has failed to reveal large-scale gene degeneration on plant Y chromosomes. Here, we uncover rapid and extensive degeneration of Y-linked genes in a plant species, Silene latifolia, that evolved sex chromosomes de novo in the last 10 million years. Previous transcriptome-based studies of this species missed unexpressed, degenerate Y-linked genes. To identify sex-linked genes, regardless of their expression, we sequenced male and female genomes of S. latifolia and integrated the genomic contigs with a high-density genetic map. This revealed that 45% of Y-linked genes are not expressed, and 23% are interrupted by premature stop codons. This contrasts with X-linked genes, in which only 1.3% of genes contained stop codons and 4.3% of genes were not expressed in males. Loss of functional Y-linked genes is partly compensated for by gene-specific up-regulation of X-linked genes. Our results demonstrate that the rate of genetic degeneration of Y-linked genes in S. latifolia is as fast as in animals, and that the evolutionary trajectories of sex chromosomes are similar in the two kingdoms. PMID:26438872

Predicting the evolution of complex networks via similarity dynamics

NASA Astrophysics Data System (ADS)

Wu, Tao; Chen, Leiting; Zhong, Linfeng; Xian, Xingping

2017-01-01

Almost all real-world networks are subject to constant evolution, and plenty of them have been investigated empirically to uncover the underlying evolution mechanism. However, the evolution prediction of dynamic networks still remains a challenging problem. The crux of this matter is to estimate the future network links of dynamic networks. This paper studies the evolution prediction of dynamic networks with link prediction paradigm. To estimate the likelihood of the existence of links more accurate, an effective and robust similarity index is presented by exploiting network structure adaptively. Moreover, most of the existing link prediction methods do not make a clear distinction between future links and missing links. In order to predict the future links, the networks are regarded as dynamic systems in this paper, and a similarity updating method, spatial-temporal position drift model, is developed to simulate the evolutionary dynamics of node similarity. Then the updated similarities are used as input information for the future links' likelihood estimation. Extensive experiments on real-world networks suggest that the proposed similarity index performs better than baseline methods and the position drift model performs well for evolution prediction in real-world evolving networks.

New thinking, innateness and inherited representation.

PubMed

Shea, Nicholas

2012-08-05

The New Thinking contained in this volume rejects an Evolutionary Psychology that is committed to innate domain-specific psychological mechanisms: gene-based adaptations that are unlearnt, developmentally fixed and culturally universal. But the New Thinking does not simply deny the importance of innate psychological traits. The problem runs deeper: the concept of innateness is not suited to distinguishing between the New Thinking and Evolutionary Psychology. That points to a more serious problem with the concept of innateness as it is applied to human psychological phenotypes. This paper argues that the features of recent human evolution highlighted by the New Thinking imply that the concept of inherited representation, set out here, is a better tool for theorizing about human cognitive evolution.

Sex Differences: A Resultant of an Evolutionary Pressure?

PubMed

Della Torre, Sara; Maggi, Adriana

2017-03-07

Spurred by current research policy, we are witnessing a significant growth in the number of studies that observe and describe sexual diversities in human physiology and sex prevalence in a large number of pathologies. Yet we are far from the comprehension of the mechanisms underpinning these differences, which are the result of a long evolutionary history. This Essay is meant to underline female reproductive function as a driver for the positive selection of the specific physiological features that explain male and female differential susceptibility to diseases and metabolic disturbances, in particular. A clear understanding of the causes underlying sexual dimorphisms in the physio-pathology is crucial for precision medicine. Copyright © 2017 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stern, Adi; Sorek, Rotem

Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. In this paper, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. Finally, the commonalities between defense mechanismsmore » suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.« less

The Emergence of Life as a First-Order Phase Transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mathis, Cole; Bhattacharya, Tanmoy; Walker, Sara Imari

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here in this paper we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase ismore » distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.« less

The Emergence of Life as a First-Order Phase Transition

DOE PAGES

Mathis, Cole; Bhattacharya, Tanmoy; Walker, Sara Imari

2017-03-01

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here in this paper we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase ismore » distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.« less

The Emergence of Life as a First-Order Phase Transition

NASA Astrophysics Data System (ADS)

Mathis, Cole; Bhattacharya, Tanmoy; Imari Walker, Sara

2017-03-01

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase is distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.